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

- i -

• i() : core::pose::rna::BasePairStep
• I : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• i : protocols::cluster::DataPoint , protocols::frag_picker::Contact
• 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_ : protocols::frag_picker::Contact
• i_next() : core::pose::rna::BasePairStep
• i_param : core::scoring::APBSConfig
• I_PARAM() : core::scoring::APBSConfig::I_PARAM
• i_str : protocols::environment::claims::DOFElement
• i_str_ : protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• i_to_a() : protocols::normalmode::NormalMode
• i_to_a_ : protocols::normalmode::NormalMode
• i_want_this_atom_to_move() : protocols::rna::movers::ErraserMinimizerMover , protocols::simple_moves::ConstrainToIdealMover
• iA() : core::scoring::TMscore
• iA_ : core::scoring::TMscore
• IAM_ : protocols::anchored_design::AnchoredDesignMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• 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::AtomInformation , core::io::ModifiedResidueInformation , core::io::ResidueInformation
• icode() : core::pose::PDBInfo
• iCode : core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• icode : core::scoring::packstat::SimplePDB_Atom , protocols::antibody::design::PDBNumbering
• icode1 : core::io::CisPeptideInformation , core::io::HELIXInformation
• iCode1 : core::io::LinkInformation
• icode1 : core::io::SHEETInformation
• iCode1 : core::io::SSBondInformation
• icode2 : core::io::CisPeptideInformation , core::io::HELIXInformation
• iCode2 : core::io::LinkInformation
• icode2 : core::io::SHEETInformation
• iCode2 : core::io::SSBondInformation
• iCode_ : core::io::ResidueInformation
• icode_ : protocols::pmut_scan::MutationData
• icoor() : core::chemical::Atom , core::chemical::MutableResidueConnection , core::chemical::MutableResidueType , core::chemical::Orbital , core::chemical::ResidueConnection , core::chemical::ResidueType , core::conformation::Residue
• icoor_ : core::chemical::Atom , core::chemical::MutableResidueConnection , core::chemical::Orbital , core::chemical::ResidueConnection , core::chemical::ResidueType
• icoor_05_2009() : core::pack::palette::PackerPalette
• icoor_05_2009_ : core::pack::palette::PackerPalette
• icoor_targets_ : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• 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::nmr::VoxelGridPoint , core::scoring::packstat::CavityBall , core::scoring::packstat::Sphere , core::scoring::PDvertex , core::scoring::power_diagram::PDvertex , core::sequence::Sequence , protocols::constraint_generator::ConstraintGenerator , protocols::denovo_design::architects::StructureArchitect , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::environment::claims::DOFElement , protocols::environment::EXCN_Env_Security_Exception , protocols::features::Segment , protocols::features::TaskOperationFeatures::Taskop_id_name_factory_ , protocols::forge::remodel::RemodelConstraintGenerator , protocols::frag_picker::VallResidue , protocols::hbnet::HBondNetStruct , protocols::indexed_structure_store::StructureEntry , protocols::jd2::archive::Batch , protocols::nmr::pcs::AtomGridPoint , protocols::optimize_weights::OptEVariableExpression
• ID : protocols::stepwise::legacy::modeler::rna::Cluster_Member
• id : protocols::stepwise::modeler::rna::Torsion_Info , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::toolbox::Node , protocols::wum::WorkUnitBase
• id2list() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• id2proftag() : protocols::abinitio::FragmentSampler
• id2proftag_ : protocols::abinitio::FragmentSampler
• id2state() : protocols::stepwise::sampler::StepWiseSamplerSizedAny
• id2string() : protocols::abinitio::FragmentSampler
• id2string_ : protocols::abinitio::FragmentSampler
• id_ : core::environment::EnvCore , core::fragment::picking_old::vall::VallResidue , core::id::EXCN_AtomNotFound , core::scoring::nmr::NMRDummySpinlabelConformer , core::scoring::nmr::VoxelGridPoint , core::scoring::packstat::CavityBall , core::scoring::PDvertex , core::scoring::power_diagram::PDvertex , core::scoring::saxs::FormFactor , core::sequence::Sequence , protocols::constraint_generator::ConstraintGenerator , protocols::denovo_design::architects::StructureArchitect , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::denovo_design::movers::AlignResiduesMover , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::environment::EXCN_Env_Security_Exception , protocols::features::strand_assembly::StrandFragment , protocols::forge::remodel::RemodelConstraintGenerator , protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::VallResidue , protocols::loop_grower::LoopPartialSolution , protocols::nmr::pcs::AtomGridPoint , protocols::optimize_weights::OptEVariableExpression , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::wum::WorkUnitBase::WU_Header
• id_exists() : protocols::calc_taskop_filters::IdManager< T >
• 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_for_resnum() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• id_from_index() : protocols::kinematic_closure::ClosureProblem
• id_list_ : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• id_list_cached_ : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• id_map_ : protocols::abinitio::abscript::AbscriptMover
• 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::HeaderInformation
• idCode_ : core::io::HeaderInformation
• ideal_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser
• ideal_abego_ : protocols::denovo_design::connection::ConnectionArchitect
• ideal_angle_about_contact_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ideal_angle_about_metal_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ideal_bond_length() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper
• ideal_bond_length_set() : core::chemical::ChemicalManager
• ideal_bond_length_sets_ : core::chemical::ChemicalManager
• ideal_contacts_ : protocols::sewing::data_storage::LigandResidue
• ideal_contacts_num : protocols::sewing::data_storage::LigandDescription
• ideal_contacts_str : protocols::sewing::data_storage::LigandDescription
• ideal_delta_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_delta_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_dihedral_3_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ideal_dihedral_about_contact_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ideal_dihedral_about_metal_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ideal_distance_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• ideal_geometry_ : protocols::minimization_packing::MinimalRotamer
• 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_repeat_ : protocols::simple_moves::RepeatPropagationMover
• ideal_sheets_ : protocols::loop_grower::SheetSampler
• ideal_val() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• ideal_val_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• ideal_xyz() : core::chemical::Atom , core::chemical::Orbital , core::chemical::ResidueType
• ideal_xyz_ : core::chemical::Atom , core::chemical::Orbital , core::chemical::ResidueType
• IdealAbegoGenerator() : protocols::denovo_design::components::IdealAbegoGenerator
• IdealBondLengthSet() : core::chemical::IdealBondLengthSet
• IdealBondLengthSets : core::chemical::ChemicalManager
• idealExtension_ : protocols::pose_length_moves::NearNativeLoopCloser
• idealize() : protocols::relax::RangeRelaxMover
• idealize_ : protocols::carbohydrates::GlycanTreeModeler , protocols::denovo_design::components::SheetDB , protocols::relax::RangeRelaxMover , protocols::seeded_abinitio::CloseFold
• idealize_and_repack_pose() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• idealize_conformers_ : protocols::match::downstream::LigandConformerBuilder
• idealize_coord_ : protocols::recces::sampler::rna::MC_RNA_Suite , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• idealize_glycan_residues() : protocols::carbohydrates::GlycanSampler
• idealize_glycosylation_ : protocols::carbohydrates::SimpleGlycosylateMover
• idealize_graft_cdrs_ : protocols::antibody::design::AntibodyDesignMover
• idealize_insert() : protocols::grafting::AnchoredGraftMover
• idealize_insert_ : protocols::grafting::AnchoredGraftMover
• idealize_loop() : protocols::loop_modeling::LoopBuilder
• idealize_loop_first_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idealize_pose() : protocols::relax::RangeRelaxMover
• idealize_proline_nvs() : core::scoring::methods::CartesianBondedEnergy
• idealize_sidechains() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• idealize_torsions_ : protocols::carbohydrates::LinkageConformerMover
• IdealizeAnomericHydrogens() : protocols::carbohydrates::IdealizeAnomericHydrogens
• IdealizeHelicesMover() : protocols::rbsegment_relax::IdealizeHelicesMover
• IdealizeMover() : protocols::idealize::IdealizeMover
• IdealizeRamaEnergy() : core::scoring::Ramachandran2B
• IdealParametersDatabase() : core::scoring::methods::IdealParametersDatabase
• ident_string_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• identical_info_consistency_check() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• identical_tag_found_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• identify_and_set_cdr_cluster() : protocols::antibody::clusters::CDRClusterSet
• identify_antibody() : protocols::antibody::AntibodyInfo
• identify_CDR_from_a_sequence() : protocols::antibody::AntibodyInfo
• identify_light_chain() : protocols::antibody::AntibodyInfo
• identify_motif_build_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• identify_motif_BuildPositions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• identify_possible_binders() : protocols::sewing::hashing::LigandBindingResPlacer
• identify_ss() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::topology::SS_Info2
• identities() : core::sequence::SequenceAlignment , protocols::task_operations::RestrictIdentitiesOperation
• identities_ : protocols::task_operations::RestrictIdentitiesOperation
• identity() : core::id::SequenceMapping
• identity_matrix() : protocols::forge::remodel::RemodelGlobalFrame , protocols::simple_filters::RepeatParameterFilter
• 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
• idl_beta_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_C_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CA_CM_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CA_CM_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CM_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CM_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_N_CA_CM_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• idl_C_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• idl_CA_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_CA_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• idl_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_N_CA_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• IDLE : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::scoring::util_methods::DumpTrajectoryEnergy
• idle() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::ArchiveManager
• IdManager() : protocols::calc_taskop_filters::IdManager< T >
• IDMoverSetMap : protocols::abinitio::abscript::AbscriptMover
• ids_ : core::scoring::SecondaryStructurePotential , protocols::loop_grower::LoopPartialSolution
• ids_initializer() : core::scoring::SecondaryStructurePotential
• ids_of_clashing_nodes_ : core::scoring::hbonds::graph::HBondNode
• ids_span_cut() : protocols::kinematic_closure::ClosureProblem
• idsn_ : core::scoring::SecondaryStructurePotential
• idsn_initializer() : core::scoring::SecondaryStructurePotential
• idx : protocols::simple_moves::AtomHashNode
• idx2cart() : core::scoring::electron_density::ElectronDensity , core::scoring::PoissonBoltzmannPotential
• idxoffset2cart() : core::scoring::electron_density::ElectronDensity
• if_dock_pert_ : protocols::docking::DockingInitialPerturbation
• if_ensemble_ : protocols::docking::DockingProtocol
• if_fit_area_ : protocols::scoring::methods::saxs::PDDFEnergy
• if_hydrogens_ : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• if_late_scoring_for_zeros() : protocols::frag_picker::scores::FragmentScoreManager
• if_metrics_ : protocols::flexpep_docking::FlexPepDockingProtocol
• if_uniform_trans_ : protocols::docking::DockingInitialPerturbation
• iface_cutoff_ : protocols::protein_interface_design::movers::LoopFinder
• ifc() : protocols::kinmatch::FunGroupTK
• ifc_ : protocols::kinmatch::FunGroupTK
• iffilters_ : protocols::filters::IfThenFilter
• ifit_ : protocols::evaluation::PCA
• IfMover() : protocols::moves::IfMover
• IfThenFilter() : protocols::filters::IfThenFilter
• ig() : protocols::multistate_design::PackingState , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• ig_ : core::pack::annealer::DebuggingAnnealer , core::pack::annealer::FASTERAnnealer , core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::annealer::FixbbPwatSimAnnealer , core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::MultiCoolAnnealer , core::pack::annealer::SequenceSymmetricAnnealer , core::pack::annealer::SmartFixbbSimAnnealer , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::hbnet::HBNet , protocols::minimization_packing::PackRotamersMover , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• ig_edge_list_ : core::pack::interaction_graph::InteractionGraphBase
• IG_edge_reweights_ : core::pack::task::PackerTask_
• ig_nodes_ : core::pack::interaction_graph::InteractionGraphBase
• ig_p_ : protocols::multistate_design::PackingState
• ig_threads_to_request() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• ig_threads_to_request_ : core::pack::task::PackerTask_
• IGEdgeReweightContainer() : core::pack::task::IGEdgeReweightContainer
• IGEdgeReweighter() : core::pack::task::IGEdgeReweighter
• IGEdgeReweights() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• IGInterfaceEdgeUpweighter() : protocols::toolbox::IGInterfaceEdgeUpweighter
• IGLigandDesignEdgeUpweighter() : protocols::toolbox::IGLigandDesignEdgeUpweighter
• ignore() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_ : protocols::denovo_design::components::StructureDataPerturber
• ignore_assignments() : protocols::noesy_assign::PeakFileFormat_Base
• ignore_assignments_ : protocols::noesy_assign::PeakFileFormat_Base
• ignore_atom_named_H() : core::chemical::ResidueTypeFinder
• ignore_atom_named_H_ : core::chemical::ResidueTypeFinder
• ignore_bb_heavy_unsats_ : protocols::simple_filters::BuriedUnsatHbondFilter
• ignore_bs_ : protocols::electron_density::ScaleMapIntensities
• ignore_burial_ : protocols::simple_filters::MembAccesResidueLipophilicityFilter
• ignore_c_terminal_SS_ : protocols::simple_filters::SSElementMotifContactFilter
• ignore_chain_ : protocols::fldsgn::CircularPermutation
• ignore_chain_break_ : protocols::splice::Splice , protocols::splice::SpliceOut
• ignore_cmdline_enzdes_cstfile() : protocols::forge::components::VarLengthBuild
• ignore_cmdline_enzdes_cstfile_ : protocols::forge::components::VarLengthBuild
• ignore_cmdline_for_build_points_ : protocols::match::MatcherTask
• ignore_correlation_after_ : protocols::ligand_docking::ProtLigEnsemble
• ignore_correlation_until_ : protocols::ligand_docking::ProtLigEnsemble
• ignore_default_docking_task_ : protocols::docking::DockingProtocol
• ignore_default_task() : protocols::docking::DockingHighRes
• ignore_default_task_ : protocols::docking::DockingHighRes
• ignore_FARFAR_no_auto_bulge_parent_tag_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ignore_FARFAR_no_auto_bulge_tag_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ignore_h_collisions() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• ignore_h_collisions_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• ignore_helix_direction_ : protocols::fldsgn::filters::HSSTripletFilter
• ignore_light_chain() : protocols::antibody::AntibodyDatabaseManager
• ignore_light_chain_ : protocols::antibody::AntibodyDatabaseManager , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• ignore_list() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_list_ : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_lists_ : protocols::tcr::TCRmodel
• ignore_loops() : protocols::fldsgn::NcontactsCalculator
• ignore_loops_ : protocols::fldsgn::NcontactsCalculator
• ignore_n_terminal_SS_ : protocols::simple_filters::SSElementMotifContactFilter
• ignore_negative_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• ignore_negative_intensity_ : protocols::noesy_assign::PeakFileFormat_Base
• ignore_pikaa_natro() : protocols::flxbb::LayerDesignOperation
• ignore_pikaa_natro_ : protocols::flxbb::LayerDesignOperation
• ignore_pose_datacache_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• ignore_pose_profile_length_mismatch_ : protocols::calc_taskop_movers::ConsensusDesignMover , protocols::task_operations::SeqprofConsensusOperation
• ignore_radius() : core::scoring::sc::ElectrostaticComplementarityCalculator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric
• ignore_radius_ : core::scoring::sc::ElectrostaticComplementarityCalculator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric
• ignore_radius_resolution_ : core::scoring::sc::ElectrostaticComplementarityCalculator
• ignore_register_shift_ : protocols::fldsgn::filters::SheetTopologyFilter
• ignore_residue() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_residues_in_csts() : protocols::idealize::IdealizeMover
• ignore_residues_in_csts_ : protocols::idealize::IdealizeMover
• ignore_resonancefile_intensities_ : protocols::noesy_assign::PeakAssignmentParameters
• ignore_resonancefile_tolerances_ : protocols::noesy_assign::PeakAssignmentParameters
• ignore_same_sheet() : protocols::fldsgn::NcontactsCalculator
• ignore_same_sheet_ : protocols::fldsgn::NcontactsCalculator
• ignore_same_sselement() : protocols::fldsgn::NcontactsCalculator
• ignore_same_sselement_ : protocols::fldsgn::NcontactsCalculator
• ignore_secstruct() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• ignore_secstruct_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• ignore_single_jump_ : protocols::symmetry::DetectSymmetry
• ignore_sugars() : core::io::StructFileRepOptions
• ignore_sugars_ : core::io::StructFileRepOptions
• ignore_surface_res_ : protocols::simple_filters::BuriedUnsatHbondFilter
• ignore_template_indices_ : protocols::hybridization::ChunkTrialMover
• ignore_terminal_res_ : protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_moves::StructProfileMover
• ignore_terminal_SS_ : protocols::simple_ddg::SSElementBisectddGFilter
• ignore_unconnected_upper() : core::select::residue_selector::PhiSelector
• ignore_unconnected_upper_ : core::select::residue_selector::PhiSelector
• ignore_unmatched_virtual_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ignore_unrecognized_res() : core::io::StructFileRepOptions
• ignore_unrecognized_res_ : core::io::StructFileRepOptions , protocols::rotamer_recovery::RotamerRecovery
• ignore_virtual_ : protocols::simple_moves::CopyDofMover
• ignore_waters() : core::io::StructFileRepOptions
• ignore_waters_ : core::io::StructFileRepOptions
• ignore_zero_byte() : protocols::simple_filters::FileExistFilter
• ignore_zero_byte_ : protocols::simple_filters::FileExistFilter
• ignore_zero_occupancy() : core::io::StructFileRepOptions
• ignore_zero_occupancy_ : core::io::StructFileRepOptions
• ignoreBuriedPockets_ : protocols::pockets::PocketGrid
• ignored() : protocols::denovo_design::components::StructureDataPerturber
• ignored_chains_ : protocols::analysis::InterfaceAnalyzerMover
• ignoreExposedPockets_ : protocols::pockets::PocketGrid
• ignorefinished() : protocols::jobdist::BaseJobDistributor
• ignorefinished_ : protocols::jobdist::BaseJobDistributor
• IgnoreSubsetConstraintSet() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• iha_cut() : protocols::mpi_refinement::MultiObjective
• iha_cut_ : protocols::mpi_refinement::MultiObjective
• iha_penalty_mode() : protocols::mpi_refinement::MultiObjective
• iha_penalty_mode_ : protocols::mpi_refinement::MultiObjective
• iha_penalty_slope() : protocols::mpi_refinement::MultiObjective
• iha_penalty_slope_ : protocols::mpi_refinement::MultiObjective
• illegal_variable_names_ : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• image_start_ : protocols::simple_moves::SymmetricFragmentMover
• implicit_lipids() : core::conformation::membrane::MembraneInfo
• implicit_lipids_ : core::conformation::membrane::MembraneInfo
• implicit_radii_set_ : core::scoring::sasa::SasaCalc
• ImplicitFastClashCheck() : protocols::scoring::ImplicitFastClashCheck
• ImplicitLipidInfo() : core::conformation::membrane::ImplicitLipidInfo
• implies : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• import() : core::kinematics::MoveMap
• import_and_set_up_native() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• import_exp_chemical_shift_data() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• import_false() : core::kinematics::MoveMap
• import_ID : core::pose::rna::VDW_RepScreenInfo
• Import_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• import_pose_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• import_tags() : protocols::rosetta_scripts::RosettaScriptsParser
• import_true() : core::kinematics::MoveMap
• importance_ : protocols::normalmode::NormalMode
• important_residues_ : protocols::switches::GraftSwitchMover
• ImportPoseOptions() : core::import_pose::ImportPoseOptions
• ImportTagName : protocols::rosetta_scripts::RosettaScriptsParser
• ImportUnboundRotamersOperation() : protocols::task_operations::ImportUnboundRotamersOperation
• impose_constraints() : protocols::idealize::IdealizeMover
• impose_constraints_ : protocols::idealize::IdealizeMover
• improper_lookup_ : core::scoring::GenericBondedPotential
• improper_parameters() : core::scoring::methods::ResidueCartBondedParameters
• improper_params_ : core::scoring::methods::ResidueCartBondedParameters
• improper_pot_ : core::scoring::GenericBondedPotential
• impropers_indep_ : core::scoring::methods::IdealParametersDatabase
• in_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• in_a_submotif() : core::pose::full_model_info::FullModelInfo
• in_a_submotif_seed() : core::pose::full_model_info::FullModelInfo
• in_bin() : core::scoring::bin_transitions::BinTransitionData
• in_bin_i() : core::scoring::bin_transitions::BinTransitionData
• in_bin_iplus1() : core::scoring::bin_transitions::BinTransitionData
• in_blacklist() : protocols::wum::WorkUnitBase
• in_charge() : protocols::loops::GuardedLoopsFromFile
• in_charge_ : protocols::loops::GuardedLoopsFromFile
• in_context() : protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter
• in_context_ : protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter
• in_FASTER_mode_ : core::pack::interaction_graph::FASTERNode
• in_fullatom() : core::io::silent::SilentFileOptions
• in_fullatom_ : core::io::silent::SilentFileOptions
• in_helix() : core::pose::rna::RNA_SecStruct
• in_list : protocols::toolbox::Node
• in_map_from_reference() : core::pose::toolbox::AtomID_Mapper
• in_membrane() : core::conformation::membrane::MembraneInfo
• in_paired_strands() : core::scoring::dssp::Dssp
• in_place_copy() : core::conformation::Conformation
• in_range_CCD_torsion : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• in_res_ : core::scoring::constraints::MembraneSpanTermZConstraint
• in_root_partition : core::pose::rna::VDW_RepScreenInfo
• in_same_helix() : core::pose::rna::RNA_SecStruct
• in_silent_score_prefix() : core::io::silent::SilentFileOptions
• in_silent_score_prefix_ : core::io::silent::SilentFileOptions
• in_silent_scores_wanted() : core::io::silent::SilentFileOptions
• in_silent_scores_wanted_ : core::io::silent::SilentFileOptions
• in_silent_scores_wanted_set() : core::io::silent::SilentFileOptions
• in_silent_scores_wanted_set_ : core::io::silent::SilentFileOptions
• in_silent_struct_type() : core::io::silent::SilentFileOptions
• in_silent_struct_type_ : core::io::silent::SilentFileOptions
• in_silent_struct_type_set() : core::io::silent::SilentFileOptions
• in_silent_struct_type_set_ : core::io::silent::SilentFileOptions
• in_span() : core::conformation::membrane::SpanningTopology
• inarray_ : core::scoring::atomic_depth::AtomicDepth
• inbound() : protocols::wum::WorkUnitManager
• inbound_wus_ : protocols::wum::WorkUnitManager
• inc_alternate_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• inc_curr_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• incident_edge_list_ : core::pack::interaction_graph::NodeBase
• incident_edge_vector_ : core::pack::interaction_graph::NodeBase
• incl_nonopt() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• incl_nonopt_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• include_ab_templates_ : protocols::tcr::TCRmodel
• include_adjacent_residues_ : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• include_all_design_targets_in_design_interface_ : protocols::enzdes::EnzdesBaseProtocol
• include_all_water() : protocols::task_operations::RestrictToInterfaceVectorOperation
• include_all_water_ : protocols::simple_task_operations::RestrictToInterface , protocols::task_operations::RestrictToInterfaceVectorOperation
• include_backbone_ : protocols::simple_filters::SidechainRmsdFilter
• include_backbone_atoms_ : protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• include_background_energies_ : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• include_bb_bb_ : protocols::residue_selectors::HBondSelector
• include_bg_ : protocols::toolbox::RotamerBoltzmannWeightEvaluator
• include_c_s_only_in_hsasa_ : core::scoring::sasa::SasaCalc
• include_cdr4_ : protocols::antibody::AntibodyCDRGrafter
• include_count_ : protocols::optimize_weights::IterativeOptEDriver
• include_cstE_ : protocols::enzdes::LigInterfaceEnergyFilter
• 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_ , protocols::protein_interface_design::movers::TryRotamers , protocols::symmetric_docking::SymRestrictTaskForDocking
• include_current_ds_ : protocols::denovo_design::DisulfidizeMover
• include_default_linear_chainbreak_ : protocols::rna::denovo::movers::RNA_Minimizer
• include_dna_potentials_in_specificity_calculations_ : protocols::dna::DnaInterfacePacker
• include_eggshell_points_based_on_known_ligand() : protocols::pockets::NonPlaidFingerprint
• include_focus_ : core::pack::task::residue_selector::ClashBasedShellSelector
• include_focus_in_subset_ : core::select::residue_selector::NeighborhoodResidueSelector
• include_gly() : core::pack::task::operation::RestrictYSDesign
• include_His_chain_terminus_ : protocols::simple_filters::InterfaceHbondsFilter
• include_hydrogens_ : core::scoring::sasa::SasaCalc
• include_loop_ss_chunks_ : protocols::hybridization::HybridizeProtocol
• include_magnetic_anisotropy_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_metals_ : protocols::enzdes::GenerateStoredRBConfs
• include_native_aa() : protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::MutationSetDesignOperation
• include_native_aa_ : protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::MutationSetDesignOperation
• include_native_restype() : protocols::task_operations::ResidueProbDesignOperation
• include_native_restype_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::task_operations::ResidueProbDesignOperation
• include_neighbor_base_stacks_ : core::pose::rna::RNA_FilteredBaseBaseInfo
• include_neighbors() : protocols::simple_task_operations::RestrictToLoopsAndNeighbors
• include_neighbors_ : protocols::antibody::H3RefineCCD , protocols::simple_task_operations::RestrictToLoopsAndNeighbors , protocols::task_operations::RestrictToMoveMapChiOperation
• include_only_center_clusters() : protocols::antibody::CDRSetOptions
• include_only_clusters() : protocols::antibody::CDRSetOptions
• include_only_clusters_ : protocols::antibody::CDRSetOptions
• include_only_clusters_add() : protocols::antibody::CDRSetOptions
• include_only_clusters_clear() : protocols::antibody::CDRSetOptions
• include_only_current_cluster() : protocols::antibody::CDRSetOptions
• include_only_end_ : protocols::scoring::methods::pcs2::PcsEnergyParameter
• include_only_end_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_end_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_end_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_end_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_germlines() : protocols::antibody::CDRSetOptions
• include_only_germlines_ : protocols::antibody::CDRSetOptions
• include_only_germlines_add() : protocols::antibody::CDRSetOptions
• include_only_germlines_clear() : protocols::antibody::CDRSetOptions
• include_only_pdb_ids_ : protocols::antibody::CDRSetOptions
• include_only_pdbs() : protocols::antibody::CDRSetOptions
• include_only_pdbs_add() : protocols::antibody::CDRSetOptions
• include_only_pdbs_clear() : protocols::antibody::CDRSetOptions
• include_only_set_depth_ : core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric
• include_only_species() : protocols::antibody::CDRSetOptions
• include_only_species_ : protocols::antibody::CDRSetOptions
• include_only_species_add() : protocols::antibody::CDRSetOptions
• include_only_species_clear() : protocols::antibody::CDRSetOptions
• include_only_start_ : protocols::scoring::methods::pcs2::PcsEnergyParameter
• include_only_start_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_start_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_start_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_start_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_probe_radius_ : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• include_protein_omega_ : core::simple_metrics::metrics::DihedralDistanceMetric
• include_proto_cdr4_ : protocols::antibody::AntibodyFeatures
• include_rama_prepro_and_proclose_ : core::simple_metrics::metrics::InteractionEnergyMetric
• include_resid() : core::pack::task::operation::RestrictYSDesign
• include_residue() : core::pack::task::operation::PreventRepacking , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictResidueToRepacking , protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::DesignAroundOperation
• include_residue_ : protocols::analysis::InterfaceAnalyzerMover
• include_residues() : protocols::hybridization::FragmentBiasAssigner
• include_residues_ : protocols::hybridization::CartesianSampler
• include_ring_current_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_rna_prot_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• include_root_ : core::select::residue_selector::GlycanResidueSelector
• include_self_ : core::simple_metrics::per_residue_metrics::HbondMetric , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric
• include_side_chains_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• include_submotifs_from_jump_library_ : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• include_subunit_ : core::conformation::symmetry::SymmData
• include_terminal_loops_ : core::select::residue_selector::SecondaryStructureSelector
• include_terms_ : protocols::optimize_weights::IterativeOptEDriver
• include_trp() : protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation
• include_trp_ : protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation
• include_type_ : protocols::simple_moves::WriteFiltersToPose
• include_virt_waters_ : core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric
• include_virtual_side_chain() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• include_virtual_side_chain_ : core::pack::task::ResidueLevelTask_
• include_water_ : protocols::analysis::PackStatMover
• IncludeCurrentRLT() : core::pack::task::operation::IncludeCurrentRLT
• included_nres_ : protocols::analysis::InterfaceAnalyzerMover
• included_properties_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• included_types_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• incoming_structures_ : protocols::abinitio::HedgeArchive
• incomplete() : core::chemical::ResConnID
• incomplete_pjns_using_input_pose_ : protocols::jd3::standard::PreliminaryLarvalJobTracker
• incorporate_batch() : protocols::abinitio::HedgeArchive
• incorporate_matches_into_pose_ : protocols::match::MatcherMover
• incorporate_motifs() : protocols::motifs::IRCollection , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• increase_chainbreak_weight_and_update_monte_carlo() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• increase_cycles_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• increase_global_count() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• increase_history_size_ : core::pack::task::operation::EnableMultiCoolAnnealer
• increase_multi_cool_annealer_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• increase_packer_residue_radius() : core::pack::rotamer_set::RotamerSetOperation , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• increase_range_to_ignore_ss_element() : protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBMover
• increasing() : protocols::loops::Loop , protocols::nonlocal::Region
• increment_accepted_hbond_count_for_group() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• increment_accepts() : protocols::recces::RECCES_Mover
• increment_both() : core::pack::interaction_graph::RotamerDots
• increment_both_and_cache() : core::pack::interaction_graph::RotamerDots
• increment_client_rank() : protocols::jd2::MPIFileBufJobDistributor
• increment_coords() : core::chemical::mainchain_potential::MainchainScoreTable
• increment_count() : core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDotsCache , protocols::stepwise::screener::StepWiseScreener
• increment_count_nodes_in_flexseg() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• increment_counts() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• increment_cur_indices() : protocols::helical_bundle::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSamplerHelper
• increment_current_job_index() : protocols::jd3::JobTracker
• increment_donated_hbond_count_for_group() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• increment_edge_list_iterator() : core::pack::interaction_graph::InteractionGraphBase
• increment_energy_coords() : core::chemical::mainchain_potential::MainchainScoreTable
• increment_f1_f2_for_atom_pair() : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• increment_failed_jobs() : protocols::jd2::JobDistributor
• increment_from_cached() : core::pack::interaction_graph::RotamerDots
• increment_helix_count() : protocols::helical_bundle::BundleGridSampler
• increment_histogram_bin() : core::scoring::orbitals::OrbitalsStatistics
• increment_index() : protocols::cyclic_peptide::TryDisulfPermutations
• increment_inner() : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• increment_outer() : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• increment_reference_pose_mapping_after_seqpos() : core::pose::Pose , core::pose::reference_pose::ReferencePose , core::pose::reference_pose::ReferencePoseSet
• increment_self_overlap() : core::pack::interaction_graph::RotamerDots , protocols::vardist_solaccess::VarSolDRotamerDots
• increment_stage() : protocols::abinitio::IterativeBase
• increment_tensor_index_recursively() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• increment_this_and_cache() : core::pack::interaction_graph::RotamerDots
• increment_unique_id() : protocols::motifs::IRCollection
• increment_upstream_only_hit_combination() : protocols::match::Matcher
• incremente_n_multi_data() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• ind() : core::scoring::hbonds::HBDerivAssigner
• indel_motif_radius() : protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter
• indel_motif_radius_ : protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter
• IndelOptimizationMover() : protocols::indel::IndelOptimizationMover
• independent_cycles() : protocols::forge::remodel::RemodelLoopMover
• independent_cycles_ : protocols::forge::remodel::RemodelLoopMover
• independent_region_selectors_ : protocols::symmetry::SetupForSequenceSymmetryMover
• independent_residues() : core::conformation::symmetry::SymmetryInfo
• independent_stage() : protocols::forge::remodel::RemodelLoopMover
• IndependentBBTorsionSRFD() : core::fragment::IndependentBBTorsionSRFD
• IndependentLoopMover() : protocols::loops::loop_mover::IndependentLoopMover
• index() : core::chemical::ResidueConnection , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOBond , core::fragment::picking_old::vall::VallSection , core::scoring::hbonds::HBond , core::scoring::motif::MotifHit , core::select::movemap::MoveMapFactory::MMResIndexAction , protocols::cartesian::CartesianAtom , protocols::dna::Reversion , protocols::enzdes::EnzdesFlexibleRegion , protocols::forge::remodel::LineObject , protocols::genetic_algorithm::EntityElement , protocols::ligand_docking::ga_ligand_dock::Pharmacophore , protocols::loophash::LeapIndex , protocols::match::upstream::ScaffoldBuildPoint , protocols::mean_field::jagged_array< T, A >
• Index : protocols::mean_field::jagged_array< T, A >
• index : protocols::mpi_refinement::MethodParams , protocols::simple_filters::SecretionPredictionFilter::tm_region , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• index1 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• index2 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• index2frac() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• index2symbol() : core::sequence::ABEGOManager , core::sequence::SSManager
• index2symbolString() : core::sequence::SSManager
• index3 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• index4 : protocols::cartesian::MD_HarmonicDihedral
• index_ : core::chemical::Element , core::chemical::ResidueConnection , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOBond , core::fragment::picking_old::vall::VallSection , core::pack::dunbrack::ProbSortClass , core::scoring::hbonds::HBond , protocols::enzdes::EnzdesFlexibleRegion , protocols::genetic_algorithm::EntityElement , protocols::kinematic_closure::ClosureSolution , protocols::ligand_docking::ga_ligand_dock::Pharmacophore , protocols::match::upstream::ScaffoldBuildPoint , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• index_and_mask_for_bin() : protocols::match::Bool3DGrid
• index_and_mask_for_point() : protocols::match::Bool3DGrid
• index_atom_map_ : core::chemical::sdf::MolFileIOMolecule
• index_file_ : protocols::simple_moves::AddResidueCouplingConstraint
• index_for_new_match() : protocols::match::output::BestMatchesCollection
• index_for_rotamer_ : protocols::match::output::UpstreamHitCacher
• index_in_vall_ : core::fragment::rna::TorsionSet
• index_mask_pair : protocols::match::Bool3DGrid
• index_of_entity() : protocols::pack_daemon::TopEntitySet
• index_pair_in_range() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• index_str_ : core::select::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_type : protocols::mean_field::jagged_array< T, A >
• index_valid() : core::chemical::sdf::MolFileIOMolecule
• IndexArray : protocols::indexed_structure_store::search::StructureData
• IndexList : core::fragment::CacheWrapper< T, XCacheUnit >
• IndexVector : protocols::evaluation::PCA
• indicate_required_context_graphs() : core::energy_methods::DEEREnergy , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::aa_repeat_energy::AARepeatEnergy , 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_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::hbonds::NPDHBondEnergy , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy , core::scoring::membrane::MPSpanAngleEnergy , core::scoring::membrane::MPSpanInsertionEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::methods::Abego , core::scoring::methods::ArgCationPiEnergy , core::scoring::methods::AromaticBackboneRestraintEnergy , core::scoring::methods::AspartimidePenaltyEnergy , core::scoring::methods::BranchEnergy , core::scoring::methods::Burial_v2Energy , core::scoring::methods::BurialEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CovalentLabelingEnergy , core::scoring::methods::CovalentLabelingFAEnergy , 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::DNA_DihedralEnergy , core::scoring::methods::DNA_EnvPairEnergy , core::scoring::methods::DNA_ReferenceEnergy , 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::GenericBondedEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HRF_MSLabelingEnergy , core::scoring::methods::HRFDynamicsEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::HydroxylTorsionEnergy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearBranchEnergy , core::scoring::methods::LinearChainbreakEnergy , 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::MotifDockEnergy , core::scoring::methods::MultipoleElecEnergy , 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::P_AA_ss_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PointWaterEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , 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::RingClosureEnergy , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SASAEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::methods::SSElementMotifContactEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::WaterSpecificEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::mhc_epitope_energy::MHCEpitopeEnergy , core::scoring::netcharge_energy::NetChargeEnergy , 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_LowResolutionPotential , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_PartitionEnergy , core::scoring::rna::RNA_StubCoordinateEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::RNP_LowResEnergy , core::scoring::rna::RNP_LowResPairDistEnergy , core::scoring::rna::RNP_LowResStackEnergy , core::scoring::rna::StackElecEnergy , core::scoring::rna::TNA_SuiteEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy , core::scoring::util_methods::DumpTrajectoryEnergy , core::scoring::vdwaals::VDW_Energy , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::membrane::scoring::FaWaterToBilayerEnergy , protocols::nmr::pcs::PCSEnergy , protocols::nmr::pre::PREEnergy , protocols::nmr::rdc::RDCEnergy , protocols::rna::AlignmentEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::SpecialRotamerEnergy , protocols::scoring::methods::TargetClashEnergy , protocols::scoring::VDW_GridEnergy
• indices() : core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs , protocols::features::BatchFeatures , protocols::features::ProtocolFeatures
• indices_ : core::chemical::NCAARotLibBBTorsions , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs , core::select::residue_selector::SliceResidueSelector
• indirect_numerator_ : protocols::qsar::scoring_grid::ChargeGrid
• individual_hbonds() : protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::task_operations::SelectByDeltaScoreOperation
• individual_hbonds_ : protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::task_operations::SelectByDeltaScoreOperation
• individual_helix_calculator() : protocols::helical_bundle::PerturbBundle
• individual_helix_calculator_cop() : protocols::helical_bundle::PerturbBundle
• individual_helix_calculators_ : protocols::helical_bundle::PerturbBundle
• individual_scale_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergyParameter
• individual_scale_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_scale_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_scale_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_scale_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_tasks_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• individual_weights_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• induce_polarizable_dipoles() : core::scoring::MultipoleElecPotential
• induced_dipole() : core::scoring::MultipoleElecResidueInfo
• induced_dipole_ : core::scoring::MultipoleElecResidueInfo
• induced_rf_dipole() : core::scoring::MultipoleElecResidueInfo
• induced_rf_dipole_ : core::scoring::MultipoleElecResidueInfo
• infer_anchor_connIDs() : protocols::generalized_kinematic_closure::GeneralizedKIC
• infer_from_pose() : protocols::denovo_design::components::StructureDataFactory
• infile() : protocols::recces::options::RECCES_Options
• infile_ : protocols::recces::options::RECCES_Options
• INFINITE_SEPARATION : core::scoring::trie::TrieCountPairBase
• infinite_vertices_ : core::scoring::power_diagram::PowerDiagram
• info() : core::scoring::ScoreFunction , protocols::moves::Mover , protocols::noesy_assign::CrossPeak
• info1_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakFileFormat_Base
• info2_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakFileFormat_Base
• info_ : protocols::moves::Mover
• info_map_ : protocols::dna::PDBOutput
• inform_edges_considered_fixedbb_substition_uncommitted() : protocols::flexpack::interaction_graph::FlexbbNode
• inform_edges_of_alt_state_before_bbjump() : protocols::flexpack::interaction_graph::FlexbbNode
• inform_incident_edges_about_partial_state_assignment() : protocols::flexpack::interaction_graph::FlexbbNode
• inform_non_changing_node_of_neighbors_change() : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• ingo_clean_ss() : protocols::simple_filters::SheetFilter
• ingo_diamers() : protocols::simple_filters::SheetFilter
• ingo_find_dir() : protocols::simple_filters::SheetFilter
• ingo_find_ord() : protocols::simple_filters::SheetFilter
• ingo_hand() : protocols::simple_filters::SheetFilter
• ingo_ident_sheets() : protocols::simple_filters::SheetFilter
• ingo_lnl() : protocols::simple_filters::SheetFilter
• ingo_locations() : protocols::simple_filters::SheetFilter
• ingo_number_of_strands() : protocols::simple_filters::SheetFilter
• ingo_proper_sheets() : protocols::simple_filters::SheetFilter
• ingo_sheet_stuff() : protocols::simple_filters::SheetFilter
• ingo_start_stop() : protocols::simple_filters::SheetFilter
• ingo_strand_dirs() : protocols::simple_filters::SheetFilter
• ingo_strand_dists_min() : protocols::simple_filters::SheetFilter
• inherit_cuts() : protocols::environment::Environment
• inherit_scorefxn_temperature() : protocols::simple_moves::sidechain_moves::SidechainMCMover
• inherit_scorefxn_temperature_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• init() : core::chemical::AtomProperties , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::rings::RingConformerSet , core::pose::Pose , core::pose::rna::RNA_IdealCoord , core::pose::rna::RNA_SuiteName , core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::carbohydrates::OmegaPreferencesFunction , 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::ElectrostaticComplementarityCalculator , core::scoring::sc::MolecularSurfaceCalculator
• init() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::MembraneAbinitio , protocols::abinitio::Protocol , protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::RefineBetaBarrel , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::constel::ExcludedFilter , protocols::constel::FilterByProxTerm , protocols::constel::FilterBySASA , protocols::constel::HBondCommon , protocols::constel::SingResCnlCrea , protocols::constraints_additional::BindingSiteConstraint , protocols::cyclic_peptide::PeptideStubMover , protocols::docking::DockingHighRes , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMProtocol , protocols::docking::TemperedDocking , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::VoxelSpacingRefinementMover , protocols::enzymatic_movers::EnzymaticMover , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentSwap , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::remodel::RemodelConstraintGenerator , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::FragmentBiasAssigner , protocols::hybridization::HybridizeProtocol , protocols::hybridization::InsertChunkMover , protocols::hybridization::MRMover , protocols::hydrate::Hydrate , protocols::indexed_structure_store::search::StructurePairQuery , protocols::jumping::MembraneJump , protocols::loop_modeling::utilities::TrajectoryLogger , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::Loops , protocols::match::output::MatchScoreWriter , protocols::md::MDBase , protocols::mean_field::AAMatrix , protocols::mean_field::RotMatrix , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::moves::ReplicaExchangeMC , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pockets::PocketConstraint , protocols::pockets::PocketGrid , protocols::recces::sampler::MC_Any , protocols::recces::sampler::MC_Comb , protocols::recces::sampler::MC_OneTorsion , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_OneJump , protocols::recces::sampler::rna::MC_RNA_Sugar , protocols::recces::sampler::rna::MC_RNA_Suite , protocols::seeded_abinitio::SegmentHybridizer , protocols::sic_dock::SICFast , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RingConformationMover , protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib , protocols::splice::RBInMover , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetry::SequentialSymmetrySlider , protocols::task_operations::RestrictToMoveMapChiOperation , protocols::toolbox::GreedyKCenter , protocols::toolbox::InteratomicVarianceMatrix , protocols::toolbox::KCluster , protocols::toolbox::KMedoid , protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::SamplerPlusPlus
• INIT : protocols::topology_broker::claims::DofClaim
• init() : protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• init_ : core::scoring::MembraneTopology , protocols::electron_density::BfactorFittingMover , protocols::simple_moves::WaterRotsDB
• init_aa_matrix() : protocols::mean_field::DesignMeanField
• init_ab_info() : protocols::antibody::design::AntibodyDesignMover
• init_acc_mapping() : core::scoring::geometric_solvation::DatabaseOccSolEne
• init_after_reading() : protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TopologyClaimer
• init_all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_allowed_pos() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• init_amp_scaling_factors() : core::scoring::geometric_solvation::OccludedHbondSolEnergy
• init_angle() : protocols::matdes::GetRBDOFValues
• init_angle_ : protocols::matdes::GetRBDOFValues
• init_apply() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• init_atom_equiv() : protocols::comparative_modeling::ThreadingMover
• init_atom_occ_mapping() : core::scoring::geometric_solvation::DatabaseOccSolEne
• init_atype_maps() : core::scoring::packing::HolesParams
• init_bbgmover() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• init_burial_filter() : protocols::switches::GraftSwitchMover
• init_calibrator() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::StructureDependentPeakCalibrator
• init_centroids() : protocols::make_rot_lib::MakeRotLibMover
• init_clash_check() : protocols::scoring::ImplicitFastClashCheck
• init_constructor() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• init_cst_score_types() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• init_d77_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_d77_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• init_data() : protocols::analysis::InterfaceAnalyzerMover
• init_defaults() : core::conformation::symmetry::SymmetryInfo
• init_disp() : protocols::matdes::GetRBDOFValues
• init_disp_ : protocols::matdes::GetRBDOFValues
• init_dist_map() : core::kinematics::ShortestPathInFoldTree
• init_dna_bform_data() : core::scoring::dna::DNABFormPotential
• init_dna_torsion_parameters() : core::scoring::dna::DNATorsionPotential
• init_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_don_mapping() : core::scoring::geometric_solvation::DatabaseOccSolEne
• init_fa_ : protocols::abinitio::ResolutionSwitcher
• init_fade_functions() : core::scoring::rna::RNA_TorsionPotential
• init_fast() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• init_ff() : core::scoring::saxs::SAXSEnergy
• init_flex_cter_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_for_equal_operator_and_copy_constructor() : protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::ResidueProbDesignOperation , protocols::task_operations::RestrictToMoveMapChiOperation
• init_for_input_yet_ : protocols::anchored_design::AnchoredDesignMover , protocols::antibody_legacy::AntibodyModeler , protocols::floppy_tail::FloppyTailMover , protocols::splice::TailSegmentMover
• init_from_blueprint() : protocols::fldsgn::potentials::SetSecStructEnergies
• init_from_cmd() : protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::SlideIntoContact , protocols::loophash::WorkUnit_LoopHash , protocols::membrane::AddMembraneMover , protocols::membrane::HelixFromSequence , protocols::membrane::MPLipidAccessibility , protocols::membrane::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::RotationMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::mpi_refinement::WorkUnit_Sampler , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover
• init_from_cml() : core::scoring::nmr::NMRDummySpinlabelEnsemble , core::scoring::nmr::NMRSpinlabel , core::scoring::nmr::pcs::PCSData , core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PREMultiSet , core::scoring::nmr::pre::PRESingleSet , core::scoring::nmr::rdc::RDCMultiSet
• init_from_comand_line() : core::pack::task::operation::OptH
• init_from_command_line_ : core::pack::task::operation::OptH
• init_from_database_file() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• init_from_decoy_set() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• init_from_file() : core::kinematics::MoveMap , core::pack::rotamers::SingleLigandRotamerLibrary , core::scoring::methods::Burial_v2Energy , core::scoring::methods::BurialEnergy , core::scoring::methods::CovalentLabelingEnergy , core::scoring::methods::CovalentLabelingFAEnergy , core::scoring::methods::HRF_MSLabelingEnergy , core::scoring::methods::HRFDynamicsEnergy , protocols::helical_bundle::BundleParametrizationCalculator , protocols::simple_filters::PredictedBurialEvaluator
• init_from_filedata() : core::scoring::nmr::pre::PRESingleSet
• init_from_ligand() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• init_from_ligand_pharmacophore() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• 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_maps() : protocols::rosetta_scripts::XmlObjects
• init_from_options() : core::import_pose::ImportPoseOptions , core::io::StructFileReaderOptions , core::io::StructFileRepOptions , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::features::strand_assembly::StrandBundleFeatures , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::tcr::TCRmodel
• init_from_pcs_filedata() : core::scoring::nmr::pcs::PCSSingleSet
• init_from_pose() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• init_from_pre_singleset_vec() : core::scoring::nmr::pre::PREMultiSet
• init_from_rdc_filedata() : core::scoring::nmr::rdc::RDCMultiSet , core::scoring::nmr::rdc::RDCSingleSet
• init_from_receptor() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• init_from_vector() : core::pack::rotamers::SingleLigandRotamerLibrary
• init_hASA_variables() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• init_hbond_data() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• init_interface_analyzer() : protocols::monte_carlo::MonteCarloInterface
• init_jd() : protocols::jd2::JobDistributor
• init_jumps() : protocols::topology_broker::FragmentJumpClaimer
• init_k48r_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_k48r_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• init_kic_loop() : protocols::simple_moves::BBGaussianMover
• init_length() : core::fragment::Frame
• init_matrix() : core::sequence::NWAligner
• init_mc() : protocols::docking::DockMCMCycle , protocols::loops::loop_closure::ccd::LoopClosure
• init_membrane_center_normal() : core::scoring::MembranePotential
• init_mini_pose() : protocols::jumping::ResiduePairJump
• init_minmover() : protocols::pose_metric_calculators::RotamerBoltzCalculator
• init_modules_amino_acids() : core::kinematics::jacobian::SeriesJacobians
• init_monoub_all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_monoub_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_monoub_flex_cter_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_mover_ : protocols::topology_broker::FragmentJumpClaimer
• init_objects() : protocols::carbohydrates::GlycanSampler
• init_on_new_input() : protocols::analysis::InterfaceAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::antibody_legacy::AntibodyModeler , protocols::floppy_tail::FloppyTailMover
• init_option() : protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField
• init_option_ : protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField
• init_options() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifDnaPacker , protocols::motifs::MotifSearch
• init_overlap_sequence_ : protocols::pose_creation::MergePDBMover
• init_parameters() : protocols::motif_grafting::movers::MotifGraftMover
• init_params() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• init_patches_from_commandline() : core::chemical::GlobalResidueTypeSet
• init_patches_from_database() : core::chemical::GlobalResidueTypeSet
• init_pcs_data_from_file() : core::scoring::nmr::pcs::PCSData
• init_pcs_values_from_file() : protocols::qsar::scoring_grid::PCSSingleGrid
• init_per_residue_data() : protocols::analysis::InterfaceAnalyzerMover
• init_pose() : protocols::abinitio::ResolutionSwitcher , protocols::mpi_refinement::MultiObjective
• init_pose_ : protocols::abinitio::ResolutionSwitcher , protocols::mpi_refinement::MultiObjective , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• init_pose_obj_ : protocols::abinitio::AbrelaxApplication
• init_posehash() : core::pose::xyzStripeHashPose
• init_potentials_from_rna_torsion_database_files() : core::scoring::rna::RNA_TorsionPotential
• init_pre_data_from_file() : core::scoring::nmr::pre::PREData
• init_PredErrorSurface() : protocols::sparta::Sparta::SpartaLib
• init_pucker_ : protocols::recces::sampler::rna::MC_RNA_Suite
• init_radical_atom_weights_and_coordinates() : core::scoring::nmr::NMRSpinlabel
• init_rama_sampling_table() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• init_rdc_data_from_file() : core::scoring::nmr::rdc::RDCData
• init_rdcs() : protocols::simple_filters::SelectRDC_Evaluator
• init_res_list() : core::scoring::methods::ReferenceEnergyNoncanonical
• init_residue_from_other() : core::conformation::Residue
• init_restypes_from_commandline() : core::chemical::GlobalResidueTypeSet
• init_restypes_from_database() : core::chemical::GlobalResidueTypeSet
• init_rna_torsion_gaussian_parameters() : core::chemical::rna::RNA_FittedTorsionInfo
• init_rot_to_pack() : protocols::pose_metric_calculators::RotamerBoltzCalculator
• init_rotamer_recovery_with_options() : protocols::rotamer_recovery::RotamerRecovery
• init_rotamers() : protocols::make_rot_lib::MakeRotLibMover
• init_SASA_radii_from_database() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• init_score_cut_ : protocols::cryst::DockLatticeMover
• init_scorefxn_ : protocols::hbnet::HBNet
• init_sequence() : protocols::evolution::NucleotideMutation
• init_sequence_ : protocols::evolution::NucleotideMutation
• init_spinlabel_name() : core::scoring::nmr::NMRSpinlabel
• init_SS_stub_HashedFragmentStore() : protocols::indexed_structure_store::SSHashedFragmentStore
• init_standard() : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• init_strength() : protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• init_structure_store() : protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::indexed_structure_store::movers::SegmentSequenceProfileMover
• init_subsidiary_constraints() : core::scoring::constraints::BasePairConstraint
• init_tag_is_done_ : protocols::rna::setup::RNA_MonteCarloJobDistributor
• init_task() : protocols::pose_metric_calculators::RotamerBoltzCalculator , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• init_task_factory_ : protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::LoopRlxMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• init_temp : protocols::rbsegment_relax::RBSegmentRelax
• init_temp_ : protocols::antibody::H3RefineCCD
• init_to_self_mapping() : core::scoring::geometric_solvation::DatabaseOccSolEne
• init_torsions_ : protocols::recces::sampler::rna::MC_RNA_Suite
• init_type() : core::sequence::MatrixScoringScheme
• init_uniform_sampling_table() : core::scoring::Ramachandran
• init_with_options() : protocols::backrub::BackrubMover , protocols::rotamer_recovery::RotamerRecovery
• init_with_pose() : protocols::sic_dock::xyzStripeHashPoseWithMeta
• initForEqualOperatorAndCopyConstructor() : protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::docking::DockingProtocol , protocols::loops::loop_mover::LoopMover
• initHBond() : protocols::sparta::PDB
• initial_angle_perturb_ : protocols::ligand_docking::Transform
• initial_asymm_foldtree_ : protocols::hybridization::HybridizeFoldtreeDynamic
• initial_cluster_set_size_ : protocols::pose_selectors::ClusterPoseSelector
• initial_constrained_residues() : protocols::simple_moves::RepeatPropagationMover
• initial_cter_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• initial_decoy_stddev_ : protocols::optimize_weights::PNatStructureOptEData
• initial_density_ : protocols::simple_moves::PeriodicBoxMover
• initial_pack_ : protocols::backrub::BackrubProtocol
• initial_perturb_ : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• initial_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• initial_phis : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• initial_pool_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• initial_pose : protocols::vip::VIP_Mover
• initial_pose_setup() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• initial_psis : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• initial_repack() : protocols::ub_e2c::ubi_e2c_modeler
• initial_rms : protocols::relax::SRelaxPose
• initial_sampling() : protocols::residue_optimization::MetapatchEnumeration
• initial_score : protocols::relax::SRelaxPose
• initial_structures_provided() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• initial_structures_provided_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• initial_temp_ : protocols::loop_modeling::LoopProtocol
• initial_template_index_ : protocols::hybridization::FoldTreeHybridize
• initial_torsions_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• initial_values_ : protocols::qsar::qsarOptFunc
• initialization_state_ : protocols::dna::DnaInterfacePacker
• initialize() : core::chemical::AtomTypeDatabaseIO , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::ResidueDatabaseIO , core::conformation::symmetry::SymmetryInfo , core::fragment::AnnotatedFragData , core::import_pose::libraries::BasePairStepLibrary , 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::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::NPDHBSimpleNode , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pose::toolbox::AtomID_Mapper , core::pose::toolbox::AtomLevelDomainMap , 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::lkball::LKB_ResidueInfo , core::scoring::lkball::LKB_ResPairMinData , core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::LinearBranchEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::MultipoleElecResPairMinData , core::scoring::methods::ProQ_Energy , core::scoring::methods::VdWTinkerResPairMinData , core::scoring::MultipoleElecPoseInfo , core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleElecRotamerSetInfo , 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::scoring::VdWTinkerPoseInfo , core::scoring::VdWTinkerResidueInfo , core::scoring::VdWTinkerRotamerSetInfo , core::select::util::SelectResiduesByLayer , core::sequence::ABEGOManager , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::cluster::calibur::Clustering , protocols::cryst::DockLatticeMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::environment::ClientMover , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::features::ProteinSilentReport , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FilterStructs , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frag_picker::SidechainContactDistCutoff , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::indexed_structure_store::search::StructureData , protocols::indexed_structure_store::search::StructureDatabase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::ligand_docking::ga_ligand_dock::LigandConformer , protocols::loops::loop_mover::LoopCM , protocols::match::downstream::ActiveSiteGrid , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::monte_carlo::GenericMonteCarloMover , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::MoveMapMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::pack_daemon::IterativeVectorExpression , protocols::pockets::PocketGrid , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::rbsegment_relax::RBSegmentRelax , protocols::recces::RECCES_Mover , protocols::rigid::UniformRigidBodyCM , protocols::rna::denovo::coarse::MultipleDomainMover , protocols::rna::denovo::movers::RNP_HighResMover , protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::rna::setup::RNA_CSA_JobDistributor , protocols::rna::setup::RNA_JobDistributor , protocols::rna::setup::RNA_MonteCarloJobDistributor , protocols::scoring::InterfaceInfo , protocols::simple_ddg::DdGScan , protocols::simple_filters::ResidueDepthCalculator , protocols::simple_filters::ResidueDepthFilter , protocols::simple_moves::WaterRotsDB , protocols::stepwise::modeler::align::StepWisePoseAligner , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::stepwise::monte_carlo::submotif::SubMotifLibrary , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• initialize_acc_strength() : core::scoring::hbonds::HBondDatabase
• initialize_active_site_definition_from_command_line() : protocols::match::MatcherTask
• initialize_active_site_grid() : protocols::match::Matcher
• initialize_actual_rep_cutoff() : protocols::stepwise::screener::PartitionContactScreener
• initialize_all_atoms() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• initialize_and_check() : core::select::residue_selector::BinSelector
• initialize_and_sample_loops() : protocols::hybridization::HybridizeProtocol
• initialize_atom_atom_overlap_cache() : core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_atom_atom_overlaps() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• initialize_atom_numbers_for_backbone_score_calculations() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_atom_numbers_sugar() : core::scoring::rna::data::RNA_DataBackboneEnergy
• initialize_auto_tune_cluster_rmsds() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialize_base_centroids_and_stubs() : core::scoring::rna::RNA_CentroidInfo
• Initialize_base_stub_list() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• initialize_bb_hbonds_graph() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• initialize_betaresidue_minima() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• 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_bump_grids() : protocols::match::Matcher
• initialize_by_dimer_pairs() : protocols::fldsgn::topology::StrandPairingSet
• initialize_by_prepack() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• initialize_by_sspair_string() : protocols::fldsgn::topology::StrandPairingSet
• initialize_by_sspair_string_and_abego() : protocols::fldsgn::topology::StrandPairingSet
• initialize_carbohydrate_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_carbontypes_to_linearize_fasol() : core::scoring::etable::Etable
• initialize_cdr_set() : protocols::antibody::design::AntibodyDesignMover
• initialize_charged_residue_map() : protocols::simple_filters::InterfaceHbondsFilter
• initialize_checkers() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_checkpointing() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• initialize_chunks() : protocols::nonlocal::SingleFragmentMover
• initialize_cluster_list() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialize_conformers() : protocols::match::downstream::LigandConformerBuilder
• initialize_constraint_forest() : protocols::abinitio::AbrelaxApplication
• initialize_constraints() : protocols::rna::denovo::RNA_DeNovoProtocol , protocols::stepwise::modeler::StepWiseModeler
• initialize_constraints_from_file() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• initialize_corresponding_atom_id_map() : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialize_cross_chain() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• initialize_cross_jump() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• initialize_curstate_graph() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• initialize_cuts() : protocols::topology_broker::TopologyBroker
• initialize_daemon_with_all_states() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• initialize_data() : core::import_pose::libraries::BasePairStepLibrary , protocols::helical_bundle::BackboneGridSamplerHelper
• initialize_data_map() : protocols::rosetta_scripts::RosettaScriptsParser
• initialize_database() : protocols::features::ReportToDB
• initialize_default_calculator_from_default_crick_params_file() : protocols::helical_bundle::MakeBundle
• initialize_defaults() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• initialize_derived_data() : core::chemical::ResidueType
• initialize_distance_range() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• initialize_DMS_low_resolution_potential() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• initialize_DMS_potential() : core::scoring::rna::data::RNA_DMS_Potential
• initialize_dofs() : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• initialize_don_strength() : core::scoring::hbonds::HBondDatabase
• initialize_dot_coords() : core::pack::interaction_graph::RotamerDots
• initialize_downstream_algorithms() : protocols::match::Matcher
• initialize_dun02_aa_parameters() : core::pack::dunbrack::RotamerLibrary
• initialize_energy_method() : core::energy_methods::DEEREnergy
• initialize_enzdes_input_data_from_command_line() : protocols::match::MatcherTask
• initialize_enzdes_input_data_with_mcfi_list() : protocols::match::MatcherTask
• initialize_espGrid() : protocols::pockets::ElectrostaticpotentialGrid
• initialize_euler_angle_grid_parameters() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_evaluator() : protocols::stepwise::screener::PartitionContactScreener
• initialize_exchange_schedule_from_file() : protocols::canonical_sampling::HamiltonianExchange
• initialize_extra_rotamer_flags_from_command_line() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• initialize_extra_rotamer_flags_from_options() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• initialize_filter() : protocols::flxbb::FlxbbDesign
• initialize_for_de_novo_generation() : core::chemical::mainchain_potential::MainchainScoreTable
• initialize_for_de_novo_protocol() : protocols::rna::denovo::RNA_DeNovoPoseInitializer
• initialize_for_farna_optimizer() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• initialize_for_movie() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• initialize_frag_source_pose() : protocols::rna::denovo::coarse::CoarseRNA_Fragments
• initialize_fragments() : protocols::seeded_abinitio::CloseFold
• initialize_free_and_fixed() : protocols::optimize_weights::IterativeOptEDriver
• initialize_from() : core::scoring::ScoreFunctionInfo
• initialize_from_atomset() : core::scoring::etable::MembEtable
• initialize_from_blueprint() : protocols::fldsgn::SheetConstraintGenerator
• initialize_from_command_line() : core::import_pose::options::RNA_BasicOptions , core::import_pose::options::RNA_DeNovoProtocolOptions , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::options::RNA_MinimizerOptions , core::import_pose::RNA_DeNovoSetup , core::pack::rotamer_set::UnboundRotamersOperation , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , protocols::match::MatcherTask , protocols::recces::options::RECCES_Options , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• initialize_from_correspondence_file() : protocols::pack_daemon::EntityCorrespondence
• initialize_from_directory() : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover , protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• initialize_from_enzcst_io() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• initialize_from_enzcst_io_and_invrots() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• initialize_from_file() : core::scoring::aa_composition_energy::AACompositionConstraint , core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::mhc_epitope_energy::MHCEpitopeConstraint , core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup , core::scoring::netcharge_energy::NetChargeConstraint , core::scoring::netcharge_energy::NetChargeEnergySetup , core::scoring::ScoreFunction , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::match::Matcher
• initialize_from_file_contents() : core::pack::palette::CustomBaseTypePackerPalette , core::scoring::aa_composition_energy::AACompositionConstraint , core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::mhc_epitope_energy::MHCEpitopeConstraint , core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup , core::scoring::netcharge_energy::NetChargeConstraint , core::scoring::netcharge_energy::NetChargeEnergySetup , protocols::helical_bundle_predict::HBPHelixAssignments
• initialize_from_file_contents_and_check() : core::select::residue_selector::BinSelector
• initialize_from_global_options() : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• initialize_from_gridlig_file() : protocols::match::downstream::ActiveSiteGrid
• initialize_from_input_atomset() : core::scoring::etable::Etable
• initialize_from_input_file() : protocols::pack_daemon::DynamicAggregateFunctionDriver , protocols::pack_daemon::EntityFunc
• initialize_from_json() : core::scoring::loop_graph::evaluator::SixDTransRotPotential
• initialize_from_jump_library() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• initialize_from_matcher_task() : protocols::match::output::OutputWriter , protocols::match::output::PDBWriter
• initialize_from_options() : core::import_pose::options::RNA_BasicOptions , core::import_pose::options::RNA_DeNovoProtocolOptions , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::options::RNA_MinimizerOptions , core::import_pose::RNA_DeNovoSetup , core::pack::dunbrack::RotamerLibrary , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::etable::EtableOptions , 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 , protocols::coupled_moves::CoupledMovesProtocol , protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication , protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions , protocols::minimization_packing::PackRotamersMover , protocols::rna::movers::ErraserMinimizerMover , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator , protocols::sewing::hashing::Hasher
• initialize_from_options_collection() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions
• initialize_from_params() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• initialize_from_pose() : core::pose::toolbox::AtomID_Mapper
• initialize_from_residue() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::toolbox::match_enzdes_util::LigandConformer
• initialize_from_residue_type() : protocols::match::upstream::UpstreamResTypeGeometry
• initialize_from_residues() : core::scoring::ResiduePairNeighborList
• initialize_from_rotation_matrix() : protocols::stepwise::sampler::rigid_body::EulerAngles
• initialize_from_tag() : core::import_pose::options::RNA_BasicOptions , core::import_pose::options::RNA_DeNovoProtocolOptions , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::options::RNA_MinimizerOptions , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• initialize_from_task() : core::pack::annealer::SmartFixbbSimAnnealer , protocols::match::Matcher
• 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::AROMATIC , core::pack::task::AUTO , core::pack::task::CHARGED , 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::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::POLAR , core::pack::task::PROPERTY , core::pack::task::ResfileCommand , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::USE_INPUT_SC
• initialize_full_model_parameters() : core::import_pose::FullModelPoseBuilder
• initialize_full_rigid_body_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_func() : core::scoring::func::GaussianChainFunc
• initialize_further_from_options() : core::import_pose::FullModelPoseBuilder
• initialize_generic_polymer_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_ghost_pose() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• initialize_global_options_from_file_contents() : protocols::helical_bundle_predict::HBPHelixAssignments
• initialize_graph_for_packing() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• initialize_graph_for_scoring() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• initialize_graphs() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• initialize_hashmap() : protocols::sewing::hashing::Hasher
• initialize_HBEval() : core::scoring::hbonds::HBondDatabase
• initialize_HBFadeInterval() : core::scoring::hbonds::HBondDatabase
• initialize_hbond_graph() : protocols::hbnet::HBNet
• initialize_HBPoly1D() : core::scoring::hbonds::HBondDatabase
• initialize_helices_from_file_contents() : protocols::helical_bundle_predict::HBPHelixAssignments
• initialize_implicit_lipid_parameters() : core::conformation::membrane::ImplicitLipidInfo
• initialize_input_poses_from_options() : core::import_pose::FullModelPoseBuilder
• initialize_inputs_from_options() : core::import_pose::RNA_DeNovoSetup
• initialize_internal_correspondence_data() : protocols::minimization_packing::GreenPacker
• initialize_internal_data() : protocols::enzdes::ResidueConformerFilter
• initialize_intrascale() : core::scoring::FACTSRsdTypeInfo
• initialize_is_fixed_res() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• Initialize_is_virtual_base() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• initialize_libraries() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• initialize_library() : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• initialize_ligand_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_ligand_from_options() : protocols::coupled_moves::CoupledMovesProtocol
• initialize_lores_silent_file() : protocols::rna::denovo::RNA_DeNovoProtocol
• initialize_map_helix_pairings_ : protocols::fldsgn::topology::HelixPairingSet
• initialize_matrix() : core::scoring::bin_transitions::BinTransitionCalculator
• initialize_max_memory_pose_num() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• initialize_membrane_residue() : protocols::membrane::AddMembraneMover
• initialize_methods_arrays() : core::scoring::ScoreFunction
• initialize_minimizer() : core::import_pose::RNA_HelixAssembler
• initialize_modeler_scorefxn() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• initialize_more_precise_base_pair_cutoffs() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_movemap() : protocols::relax::RelaxProtocolBase
• initialize_movers() : protocols::docking::DockingLowResEnsemble , protocols::rna::denovo::RNA_FragmentMonteCarlo
• initialize_moving_residue_pose_list() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_name_map() : core::pose::datacache::CacheableDataType
• initialize_next_suite_atoms() : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• initialize_NM_for_movemap() : protocols::normalmode::NormalModeRelaxMover
• initialize_node() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• initialize_non_terminal_types() : core::pack::palette::PackerPalette
• initialize_num_neighbors_counting_self() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• initialize_o2prime_green_packer() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• initialize_o2prime_packer_task() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• initialize_objects() : protocols::calc_taskop_movers::CreateSequenceMotifMover
• initialize_occupied_space_bounding_box_from_command_line() : protocols::match::MatcherTask
• initialize_occupied_space_hash() : protocols::match::Matcher
• initialize_optE_type_name_map() : protocols::optimize_weights::OptEPositionDataFactory
• initialize_orientation_atoms_from_command_line() : protocols::match::MatcherTask
• initialize_output_options_from_command_line() : protocols::match::MatcherTask
• initialize_overlap_cache() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• initialize_overlap_with_background() : core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_pack_daemons() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• initialize_packer() : protocols::recon_design::FindConsensusSequence , protocols::stepwise::modeler::packer::StepWiseMasterPacker
• initialize_packer_palette_from_global_defaults() : core::pack::palette::PackerPaletteFactory
• initialize_parameters() : core::scoring::FACTSRsdTypeInfo , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainGeneralFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::sequence::ProfSimScoringScheme , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::StepWiseMinimizer
• initialize_parameters_and_input() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialize_pcs_data_from_input_file() : protocols::qsar::scoring_grid::PCSMultiGrid
• initialize_peptide_bonded_pair_indices() : core::scoring::PolymerBondedEnergyContainer
• initialize_phi_psi_offsets() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• initialize_phosphate_move_list() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• initialize_pose() : protocols::features::ReportToDB , protocols::ncbb::SecStructFinder , protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_pose_for_rotset_creation() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• initialize_pose_for_rotsets_creation() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::pack_basic::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• initialize_pose_from_streams() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• initialize_pose_if_empty() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• initialize_pose_level_screeners() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_pose_variants_for_chain_closure() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• initialize_potential_from_file() : core::scoring::rna::RNA_TorsionPotential
• initialize_probabilities() : protocols::nonlocal::BiasedFragmentMover
• initialize_protein_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_protein_packer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_quick_alignment_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• initialize_rama_sampling_tables() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• initialize_random_chunks() : core::import_pose::libraries::RNA_ChunkLibrary
• initialize_rb_fragments() : protocols::rbsegment_relax::FragInsertAndAlignMover
• initialize_refinement_pattern() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• initialize_relax_scripts_in_database() : protocols::relax::RelaxScriptManager
• initialize_relevant_pdb_components() : core::chemical::ResidueTypeFinder
• initialize_relevant_residues() : protocols::features::ReportToDB
• initialize_repeat_pose() : protocols::simple_moves::RepeatPropagationMover
• initialize_reporters() : protocols::features::ReportToDB
• initialize_rescoords() : protocols::match::upstream::ProteinUpstreamBuilder
• initialize_residue_level_screeners() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_residue_level_task() : core::pack::palette::PackerPalette
• initialize_residue_map_from_pose() : core::pose::reference_pose::ReferencePose
• initialize_residue_type() : core::scoring::lkball::LKBallDatabase
• initialize_residues() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• initialize_residues_for_type() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• initialize_resources_for_preliminary_job_nodes() : protocols::rosetta_scripts::RosettaScriptsJobQueen
• initialize_rigid_body_movers() : protocols::rna::denovo::coarse::MultipleDomainMover
• initialize_rigid_body_rotamer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• 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_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_rna_chunk_library() : core::import_pose::libraries::RNA_ChunkLibrary
• initialize_rna_repulsive_weights() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_stagger() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rnp_aa_rna_backbone() : core::scoring::rna::RNP_LowResPotential
• initialize_rnp_base_pair() : core::scoring::rna::RNP_LowResPotential
• initialize_rnp_pair() : core::scoring::rna::RNP_LowResPotential
• initialize_rnp_pair_dist() : core::scoring::rna::RNP_LowResPairDistPotential
• initialize_rnp_stack_xy() : core::scoring::rna::RNP_LowResStackData
• initialize_rnp_vdw_parameters() : core::scoring::rna::RNA_AtomVDW
• initialize_rotamer() : protocols::features::RotamerInitializer< T, N >
• initialize_rotamer_behavior_for_residue_level_task() : protocols::ddg::ddGMover
• initialize_rotamer_set_and_scores() : protocols::ligand_docking::ga_ligand_dock::GAOptimizer
• initialize_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_samples() : protocols::helical_bundle::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSamplerHelper
• initialize_sasa_arrays() : core::pack::interaction_graph::RotamerDots , protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• initialize_scaffold_active_site_residue_list_from_command_line() : protocols::match::MatcherTask
• initialize_scaffold_build_points() : protocols::match::Matcher
• initialize_scanner() : protocols::pack_daemon::DynamicAggregateFunction
• initialize_scanner_and_function_names() : protocols::pack_daemon::EntityFunc
• initialize_score_functions() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• initialize_scorefunction() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• initialize_scorefunctions() : protocols::stepwise::modeler::StepWiseModeler
• initialize_scorefxn() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• initialize_screeners() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_secstruct() : protocols::rna::denovo::RNA_DeNovoPoseInitializer
• initialize_self_overlap() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_sequence() : protocols::topology_broker::TopologyBroker
• initialize_sequence_information() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• initialize_sf_options() : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter
• initialize_sfd_from_files_and_tags() : protocols::jd3::full_model_inputters::SilentFileFullModelInputter , protocols::jd3::pose_inputters::SilentFilePoseInputter
• initialize_sfd_from_options_and_tag() : protocols::jd3::full_model_inputters::SilentFileFullModelInputter , protocols::jd3::pose_inputters::SilentFilePoseInputter
• initialize_simulation() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicMover , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• initialize_special_behaviours() : core::pack::palette::PackerPalette
• initialize_starting_rama_scores() : protocols::loops::loop_closure::ccd::RamaCheckBase
• initialize_structure_data_from_buffer() : protocols::indexed_structure_store::search::StructureDatabase
• initialize_surface_energies() : protocols::surface_docking::SurfaceDockingProtocol
• initialize_symmetry_info() : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• initialize_tag_is_done() : protocols::rna::denovo::RNA_DeNovoProtocol
• initialize_target_evaluator() : core::scoring::cryst::PhenixInterface
• initialize_task_factory() : protocols::features::RotamerRecoveryFeatures
• initialize_task_factory_with_operations() : protocols::minimization_packing::PackRotamersMover
• initialize_task_level_behavior() : protocols::ddg::ddGMover
• initialize_tensors() : core::chemical::mainchain_potential::MainchainScoreTable
• Initialize_terminal_res() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• initialize_tna_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_tracker() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• initialize_trajectory_reporter() : protocols::features::TrajectoryReportToDB
• initialize_tree_nodes_from_enzcst_io() : protocols::toolbox::match_enzdes_util::InvrotTarget
• initialize_types_to_avoid() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• initialize_typGrid() : protocols::pockets::ElectrostaticpotentialGrid
• initialize_upstream_downstream_collision_filter_data_from_command_line() : protocols::match::MatcherTask
• initialize_upstream_nonbonded_min_separation_d2() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• initialize_upstream_residue() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• initialize_upstream_residue_collision_filter_data_from_command_line() : protocols::match::MatcherTask
• initialize_useful_info() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_value_evaluators_from_file() : protocols::enzdes::EnzdesScorefileFilter
• initialize_variables() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::options::StepWiseBasicOptions
• initialize_VDW_rep_checker() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• initialize_velocity() : protocols::md::CartesianMD
• initialize_vertex() : core::chemical::RerootRestypeVisitor
• initialize_weights() : protocols::moves::TrialMover
• initialize_with_mcfi_list() : protocols::match::MatcherTask , protocols::toolbox::match_enzdes_util::EnzConstraintIO
• initialize_worker() : protocols::boinc::Boinc
• initialize_working_parameters_and_root() : protocols::stepwise::modeler::StepWiseModeler
• initialize_xyz_grid_parameters() : protocols::stepwise::modeler::StepWiseConnectionSampler
• InitializeByBins() : protocols::simple_moves::bin_transitions::InitializeByBins
• initialized() : core::chemical::mainchain_potential::MainchainScoreTable , core::scoring::hbonds::HBondDatabase , core::scoring::lkball::LKB_ResPairMinData , core::scoring::MembraneTopology , core::scoring::methods::MultipoleElecResPairMinData , core::scoring::methods::VdWTinkerResPairMinData , core::select::residue_selector::BinSelector , protocols::branch_angle::BranchAngleOptimizer , protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfacePacker , protocols::features::ReportToDB , protocols::rbsegment_relax::RBSegment , protocols::rotamer_recovery::PerNativeRRReporterHuman
• initialized_ : core::chemical::mainchain_potential::MainchainScoreTable , core::pack::task::NOTAA , core::pack::task::PIKAA , core::pose::xyzStripeHashPose , core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondTypeManager , core::scoring::lkball::LKB_ResPairMinData , core::scoring::MembraneTopology , core::scoring::methods::MultipoleElecResPairMinData , core::scoring::methods::VdWTinkerResPairMinData , core::scoring::ScoreTypeManager , core::select::residue_selector::BinSelector , protocols::branch_angle::BranchAngleOptimizer , protocols::dna::DnaInterfaceFinder , protocols::features::ProteinSilentReport , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::loops::JSONFormattedLoopsFileReader , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::moves::StructureRestrictor , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::stepwise::modeler::align::StepWiseClusterer
• initialized_atom_id_map_for_rmsd_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialized_databases_ : core::scoring::hbonds::HBondDatabase
• initialized_pattern_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• initialized_SASA_radii : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• InitializeFromOptionCollection() : core::pack::task::operation::InitializeFromOptionCollection
• initializeSymmOps() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• InitialJumps_ : protocols::symmetry::SymmetrySlider
• initiate_voxel() : protocols::scoring::methods::TargetClashEnergy
• initOrbitalShift() : protocols::sparta::PDB
• initpara() : core::scoring::atomic_depth::AtomicDepth
• initPB() : protocols::simple_ddg::DdgFilter
• initRef() : protocols::cluster::calibur::Clustering
• inittime_ : protocols::md::CartesianMD
• inline_vector_delete() : protocols::indexed_structure_store::FragmentStore
• inName : protocols::sparta::Sparta::SpartaLib
• inNames : protocols::sparta::Sparta::SpartaLib
• inner_ : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_ , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator
• inner_cpfxn_ : core::scoring::elec::CountPairRepresentative
• inner_cycle_list_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycle_steps_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• inner_cycles_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::H3RefineCCD , protocols::docking::DockingLowRes , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::moves::RampingMover , protocols::symmetric_docking::SymDockingLowRes
• inner_end_ : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• inner_job() : protocols::jd2::Job , protocols::jd3::chunk_library::ChunkLibraryPreliminaryLarvalJob , protocols::jd3::full_model::FullModelPreliminaryLarvalJob , protocols::jd3::LarvalJob , protocols::jd3::standard::PreliminaryLarvalJob
• inner_job_ : protocols::jd2::Job , protocols::jd2::MultiThreadingJob , protocols::jd3::LarvalJob
• inner_job_nonconst() : protocols::jd2::Job
• inner_kt_ : protocols::antibody::design::AntibodyDesignMover
• inner_larval_jobs_for_curr_prelim_job_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• inner_loop() : protocols::abinitio::DoubleLayerKinematicAbinitio , protocols::abinitio::KinematicTaskControl
• inner_loop_accept_to_best_command() : protocols::relax::FastRelax
• inner_loop_counter_ : protocols::optimize_weights::IterativeOptEDriver
• inner_loop_cycles_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• inner_loop_dumpall_command() : protocols::relax::FastRelax
• inner_loop_md_command() : protocols::relax::FastRelax
• inner_loop_min_command() : protocols::relax::FastRelax
• inner_loop_ramp_repack_min_command() : protocols::relax::FastRelax
• inner_loop_reference_command() : protocols::relax::FastRelax
• inner_loop_refinement() : protocols::surface_docking::FullatomRelaxMover
• inner_loop_repack_command() : protocols::relax::FastRelax
• inner_loop_reset_reference_command() : protocols::relax::FastRelax
• inner_loop_rotamer_recovery_rate_ : protocols::optimize_weights::IterativeOptEDriver
• inner_loop_sequence_recovery_rate_ : protocols::optimize_weights::IterativeOptEDriver
• inner_mc_ : protocols::antibody::design::AntibodyDesignMover
• inner_ncycles_ : protocols::carbohydrates::GlycanSampler
• inner_radius_ : protocols::qsar::scoring_grid::AtrGrid
• inner_run_minimizer() : protocols::minimization_packing::MinMover
• InnerCycleList : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• InnerHBondMap : protocols::sparta::PDB
• inneriterations_ : core::pack::annealer::SimAnnealerBase
• inneriterations_scaling_ : core::pack::annealer::SimAnnealerBase
• InnerIterator : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• InnerJob() : protocols::jd2::InnerJob
• InnerLarvalJob() : protocols::jd3::InnerLarvalJob
• InnerMultiThreadingJob() : protocols::jd2::InnerMultiThreadingJob
• inout : core::scoring::atomic_depth::volumepixel
• inp_chi_ : protocols::make_rot_lib::RotData
• inPDB : protocols::sparta::Sparta::SpartaLib
• InPlaceIntListOP : core::pack::interaction_graph::DoubleLazyInteractionGraph
• inprogress() : protocols::jobdist::BaseJobDistributor
• inprogress_ : protocols::jobdist::BaseJobDistributor
• input_ : protocols::jd2::PoseInputStreamJobInputter , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• input_as_ref_ : protocols::hybridization::CartesianSampler
• input_code : protocols::sparta::ANN
• input_conformation() : protocols::match::upstream::OriginalBackboneBuildPoint
• input_conformation_ : protocols::match::upstream::OriginalBackboneBuildPoint
• 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_hbnet_info_residues_ : protocols::hbnet::HBNet
• input_id_ : protocols::jobdist::BasicJob
• input_initialization_pdb_numbering_setup() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• input_initialization_pdbs_ : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• input_is_angle_in_degrees_ : core::conformation::parametric::RealValuedParameter
• input_is_positive_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• input_job_result_indices() : protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob
• input_job_result_indices_ : protocols::jd3::InnerLarvalJob
• input_job_tags_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• input_loop_ : protocols::antibody::H3PerturbCCD
• input_loops_into_tuples() : protocols::anchored_design::AnchorMoversData
• input_nc_ : core::scoring::methods::CovalentLabelingEnergy , core::scoring::methods::CovalentLabelingFAEnergy , core::scoring::methods::HRFDynamicsEnergy
• input_numbering_setup() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• input_pdb_numbering_setup() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• input_pdbs_ : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• input_pose : protocols::pockets::PocketExemplarMultifunc
• input_pose_ : protocols::environment::Environment , protocols::moves::Mover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::RigidChunkClaimer
• input_pose_counter_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen , protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• input_pose_id : protocols::multistage_rosetta_scripts::ParsedTagCache
• input_pose_id_for_jobid() : protocols::multistage_rosetta_scripts::MRSJobQueen
• input_pose_index_map_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• input_pose_list_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• input_pose_no_longer_needed() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• input_pose_ONE_appended_res_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_ONE_last_appended_res_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_TWO_last_prepended_res_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_TWO_prepended_res_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_poses_ : core::import_pose::FullModelPoseBuilder , protocols::pmut_scan::PointMutScanDriver
• input_res() : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• input_res_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• input_res_initialize() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• input_res_initialize_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• input_res_vectors() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• input_res_vectors_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• input_residues_selector_ : core::select::residue_selector::ScoreTermValueBasedSelector
• input_resnum_and_chain_and_segid_ : core::import_pose::FullModelPoseBuilder
• input_rigid_core_ : protocols::topology_broker::FibrilModelingClaimer
• 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_scan_res() : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• input_scan_res_ : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• input_sequence_ : protocols::topology_broker::SequenceClaimer
• input_sequence_type_ : protocols::rna::movers::RNAThreadAndMinimizeMover
• input_set() : core::select::residue_selector::BondedResidueSelector
• input_set_ : core::select::residue_selector::BondedResidueSelector
• input_set_defined() : core::select::residue_selector::BondedResidueSelector
• input_set_defined_ : core::select::residue_selector::BondedResidueSelector , protocols::residue_selectors::HBondSelector
• input_set_selector() : core::select::residue_selector::BondedResidueSelector
• input_set_selector_ : core::select::residue_selector::BondedResidueSelector , protocols::residue_selectors::HBondSelector , protocols::residue_selectors::LigandMetalContactSelector
• input_set_selector_defined() : core::select::residue_selector::BondedResidueSelector
• input_set_str_ : core::select::residue_selector::BondedResidueSelector , protocols::residue_selectors::HBondSelector
• input_set_string() : core::select::residue_selector::BondedResidueSelector
• input_sheet_sizes_ : protocols::jumping::RandomSheetBuilder
• input_silent_files_ : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• input_silent_numbering_setup() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• input_source() : protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::features::DatabaseJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::BatchJobInputter , protocols::jd2::EmptyPoseJobInputter , protocols::jd2::JobInputter , protocols::jd2::LargeNstructJobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SerializedPoseJobInputter , protocols::jd2::SilentFileJobInputter , protocols::jd3::InnerLarvalJob , protocols::make_rot_lib::MakeRotLibJobInputter
• input_source_ : protocols::comparative_modeling::ThreadingJobInputter
• input_source_cop() : protocols::jd3::InnerLarvalJob
• input_source_for_job() : protocols::jd3::JobGenealogist
• input_source_for_node() : protocols::jd3::JobGenealogist
• input_source_id() : protocols::jd3::JGJobNode
• input_source_id_ : protocols::jd3::JGJobNode
• input_sources_ : protocols::jd3::InnerLarvalJob
• input_ss_ : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::flxbb::InterlockAroma
• input_stream_ : protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler
• input_streams_ : core::import_pose::pose_stream::MetaPoseInputStream , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler
• input_streams_with_residue_info_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• input_string : core::pose::rna::VDW_RepScreenInfo
• input_struct_definition() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• input_stub_atom0() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom0_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom1() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom1_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom2() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom2_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom3() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom3_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_tag() : protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob , protocols::jd3::InputSource , protocols::jd3::LarvalJob , protocols::jobdist::BasicJob
• input_tag_ : protocols::jd2::InnerJob , protocols::jd3::chunk_library_inputters::ChunkLibraryInputSource , protocols::jd3::full_model_inputters::FullModelInputSource , protocols::jd3::InnerLarvalJob , protocols::jd3::InputSource , protocols::jd3::pose_inputters::PoseInputSource
• input_tags_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• input_vector_expressions_ : protocols::pack_daemon::IterativeVectorExpression
• inputpose_ : protocols::rpc::JSON_RPC
• InputPoseDeallocationMessage() : protocols::jd3::deallocation::InputPoseDeallocationMessage
• InputSource() : protocols::jd3::InputSource
• inputstream : protocols::ddG::ddGData
• InputStreamStepWiseSampler() : protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler
• InputStreamWithResidueInfo() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• inputter_creator_list_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• inputter_creators_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• inputter_options_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• inputvalues_real_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• insCodes_ : protocols::pdbinfo_manipulations::SequenceSpecification
• insert() : core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , core::scoring::motif::Xfrag , core::scoring::saxs::DistanceHistogram , protocols::comparative_modeling::AlignmentSet , protocols::constraint_generator::ConstraintsMap , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frags::TorsionFragment , protocols::jd3::dag_node_managers::NodeManagerStorageMatrix , protocols::legacy_sewing::Hasher , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ScaffoldBuildPoint , protocols::protein_interface_design::movers::PlacementAuctionMover
• insert_aligned_residue() : core::id::SequenceMapping
• insert_aligned_residue_safe() : core::id::SequenceMapping
• insert_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• insert_base_pair_jumps() : protocols::rna::denovo::RNA_DeNovoPoseInitializer
• insert_chain_ending() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• insert_char() : core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• insert_chunk_into_pose() : core::import_pose::libraries::ChunkSet , core::import_pose::libraries::RNA_ChunkLibrary
• insert_conformation_by_jump() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , protocols::environment::ProtectedConformation
• insert_connected_segment() : protocols::legacy_sewing::SegmentGraph
• insert_connection_scheme() : protocols::forge::build::SegmentInsert
• insert_connection_scheme_ : protocols::forge::build::SegmentInsert
• insert_cut() : core::environment::FoldTreeSketch
• insert_ddG_rows() : protocols::features::DdGFeatures
• insert_dof_element() : protocols::environment::claims::TorsionClaim
• insert_dofs_by_residue() : protocols::simple_moves::DOFHistogramRecorder
• 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::fragment::rna::FullAtomRNA_Fragments , core::fragment::rna::RNA_Fragments , core::kinematics::AtomTree , protocols::environment::ProtectedConformation , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::rna::denovo::coarse::CoarseRNA_Fragments
• insert_gap() : core::sequence::Sequence
• insert_hbond_dehydron_row() : protocols::features::HBondFeatures
• insert_hbond_geom_coords() : protocols::features::HBondFeatures
• insert_hbond_lennard_jones_row() : protocols::features::HBondFeatures
• insert_hbond_row() : protocols::features::HBondFeatures
• insert_hit() : protocols::match::HitHasher
• insert_hit_geometry() : protocols::match::OccupiedSpaceHash
• insert_ideal_geometry_at_polymer_bond() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• insert_ideal_geometry_at_residue_connection() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• insert_into_cache() : protocols::qsar::scoring_grid::GridManager
• insert_jump() : core::environment::FoldTreeSketch
• insert_loop_at_index() : protocols::loops::LoopsFileData
• insert_map() : protocols::simple_moves::FragmentMover
• insert_map_ : protocols::rna::denovo::movers::RNA_FragmentMover , protocols::simple_moves::FragmentMover
• insert_map_frag_size_ : protocols::rna::denovo::movers::RNA_FragmentMover
• insert_match_into_pose() : protocols::match::output::PoseMatchOutputWriter
• insert_movemap_ : protocols::grafting::AnchoredGraftMover
• insert_movemap_factory_ : protocols::grafting::AnchoredGraftMover
• insert_one_body_residue_score_rows() : protocols::features::ResidueScoresFeatures
• insert_pair() : protocols::task_operations::RestrictInterGroupVectorOperation
• insert_pdb_ : protocols::forge::remodel::RemodelMover::instruction_flags
• insert_piece() : protocols::grafting::GraftMoverBase
• insert_polymer_residue() : core::conformation::Conformation , core::kinematics::FoldTree
• insert_pos_ : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• insert_pose() : protocols::forge::build::SegmentInsert
• insert_pose_ : protocols::forge::build::SegmentInsert , protocols::loop_grower::LoopGrower
• insert_pose_torsion_override_movemap() : protocols::forge::build::SegmentInsert
• insert_pose_torsion_override_movemap_ : protocols::forge::build::SegmentInsert
• insert_position() : core::fragment::picking_old::vall::eval::EnergyEval
• insert_position_ : core::fragment::picking_old::vall::eval::EnergyEval
• insert_protein_chunk_into_pose() : core::import_pose::libraries::ChunkSet
• insert_random_protein_chunks() : core::import_pose::libraries::RNA_ChunkLibrary
• insert_random_smallestmer_per_loop() : protocols::forge::remodel::RemodelLoopMover
• insert_residue_by_atoms() : core::pose::Pose
• 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_residue_pdb_confidence_rows() : protocols::features::PdbDataFeatures
• insert_residue_pdb_identification_rows() : protocols::features::PdbDataFeatures
• insert_residue_rows() : protocols::features::ResidueFeatures
• insert_residue_scores_rows() : protocols::features::ResidueScoresFeatures
• insert_residue_total_scores_rows() : protocols::features::ResidueTotalScoresFeatures
• insert_rms() : protocols::simple_moves::ScoreMover
• insert_sampled_torsion_string_into_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• insert_score_function_method_options_rows() : core::scoring::methods::EnergyMethodOptions
• insert_score_function_weights_rows() : protocols::features::ScoreFunctionFeatures
• insert_score_type_rows() : protocols::features::ScoreTypeFeatures
• insert_single_fragment() : core::kinematics::AtomTree
• insert_site_atoms_row() : protocols::features::HBondFeatures
• insert_site_environment_row() : protocols::features::HBondFeatures
• insert_site_pdb_row() : protocols::features::HBondFeatures
• insert_site_row() : protocols::features::HBondFeatures
• insert_size() : protocols::simple_moves::FragmentMover
• insert_size_ : protocols::simple_moves::FragmentMover
• insert_source_residue() : core::id::SequenceMapping
• insert_ss_into_pose() : core::scoring::dssp::Dssp , protocols::parser::BluePrint
• insert_ss_into_pose_no_IG_helix() : core::scoring::dssp::Dssp
• insert_string_real_rows() : protocols::features::JobDataFeatures
• insert_string_rows() : protocols::features::JobDataFeatures
• insert_string_string_rows() : protocols::features::JobDataFeatures
• insert_structure_score_rows() : protocols::features::StructureScoresFeatures
• insert_target_residue() : core::id::SequenceMapping
• insert_task_operation_residue_effects_row() : protocols::features::TaskOperationFeatures
• insert_task_operations_row() : protocols::features::TaskOperationFeatures
• insert_template_frags() : protocols::abinitio::AbrelaxApplication
• insert_two_body_long_range_residue_score_rows() : protocols::features::ResidueScoresFeatures
• insert_two_body_residue_score_rows() : protocols::features::ResidueScoresFeatures
• insert_unrecognized_atoms_rows() : protocols::features::UnrecognizedAtomFeatures
• insert_unrecognized_neighbors_rows() : protocols::features::UnrecognizedAtomFeatures
• insert_unrecognized_residues_rows() : protocols::features::UnrecognizedAtomFeatures
• InsertChunkMover() : protocols::hybridization::InsertChunkMover
• insertedAfterLoopRes_ : protocols::pose_length_moves::PossibleLoop
• insertedBeforeLoopRes_ : protocols::pose_length_moves::PossibleLoop
• inserter_ : protocols::loophash::LoopHashSampler
• inserting_pdb_ : protocols::forge::remodel::RemodelMover::instruction_flags
• insertion() : protocols::parser::BluePrint
• insertion_ : protocols::parser::BluePrint
• insertion_char() : protocols::forge::build::SegmentInsert
• insertion_code() : core::pose::ResidueIndexDescriptionPDB , protocols::antibody::PDBLandmark
• insertion_code_ : core::pose::ResidueIndexDescriptionPDB , protocols::antibody::PDBLandmark
• insertion_end_residue() : protocols::forge::build::SegmentInsert
• insertion_length() : protocols::grafting::GraftMoverBase
• insertion_length_ : protocols::grafting::GraftMoverBase
• insertion_list_ : protocols::rna::movers::RNAThreadAndMinimizeMover
• insertion_point_absolute_index() : protocols::forge::build::SegmentInsert
• insertion_prob_ : protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• insertion_selector_ : protocols::fold_from_loops::utils::Nub
• insertion_start_residue() : protocols::forge::build::SegmentInsert
• insertionEndIndex : protocols::forge::remodel::RemodelWorkingSet
• insertionSize : protocols::forge::remodel::RemodelData
• insertionSS : protocols::forge::remodel::RemodelData
• insertionStartIndex : protocols::forge::remodel::RemodelWorkingSet
• insertPose : protocols::forge::remodel::RemodelData
• InsertPoseIntoPoseMover() : protocols::grafting::simple_movers::InsertPoseIntoPoseMover
• InsertResMover() : protocols::pose_length_moves::InsertResMover
• InSetExpression() : protocols::pack_daemon::InSetExpression
• InstallFarnesylMover() : protocols::farnesyl::InstallFarnesylMover
• Instance() : core::pose::metrics::CalculatorFactory
• instance() : protocols::boinc::Boinc , protocols::checkpoint::Timer , protocols::network::NetworkQueue
• instance_ : protocols::jd2::JobDistributor , protocols::loop_grower::SheetSampler , protocols::noesy_assign::PeakAssignmentParameters , protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
• instance_initialized_ : protocols::canonical_sampling::TemperingBase
• instance_node_2_file_node_ : core::pack::interaction_graph::PDInteractionGraph
• instantiate_filter() : protocols::rosetta_scripts::RosettaScriptsParser
• instantiate_mover() : protocols::rosetta_scripts::RosettaScriptsParser
• instantiate_packer_palette() : protocols::rosetta_scripts::RosettaScriptsParser
• instantiate_rampfunc() : protocols::moves::RampingMover
• instantiate_residue_if_rebuilding_bulge() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• instantiate_sugar() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• instantiate_sugar_ : protocols::stepwise::screener::SugarInstantiator
• instantiate_sugars_at_cutpoint_closed() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• instantiate_sugars_recursively() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• instantiate_taskoperation() : protocols::rosetta_scripts::RosettaScriptsParser
• instantiated_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• instantiated_phosphate_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• instantiated_some_phosphate() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• instantiated_some_phosphate_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• instruct_daemons_to_drop_entity() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• instruct_daemons_to_keep_last_entity() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• instruction_dependencies_ : protocols::forge::build::BuildManager
• instruction_file_ : protocols::antibody::design::AntibodyDesignMover
• instruction_list_ : protocols::protein_interface_design::movers::VLB
• instruction_size() : protocols::fldsgn::BluePrintBDR
• instructions_ : protocols::forge::build::BuildManager
• instructions_path_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• int64_groups : protocols::indexed_structure_store::FragmentStore
• int_buf1_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• int_radii_ : protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• int_radii_sum2_ : protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• int_radii_sum_ : protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• int_to_orientation() : protocols::denovo_design::architects::StrandArchitect
• inTab : protocols::sparta::Sparta::SpartaLib
• integration_test() : protocols::magnesium::MgScanner
• integration_test_ : protocols::magnesium::MgScanner
• integration_test_mode() : core::io::StructFileRepOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• integration_test_mode_ : core::io::StructFileRepOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• IntegrationTestBreaker() : protocols::stepwise::screener::IntegrationTestBreaker
• intensity() : protocols::noesy_assign::Resonance
• intensity_ : protocols::noesy_assign::Resonance
• inter() : core::scoring::power_diagram::SAnode , core::scoring::SAnode
• inter_ : core::scoring::power_diagram::SAnode , core::scoring::SAnode
• inter_atr_ : protocols::make_rot_lib::RotData
• inter_chain() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• inter_chain_ : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• 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_rep_ : protocols::make_rot_lib::RotData
• inter_residue_connection_partner() : core::conformation::Conformation , core::conformation::Residue
• inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• interacting_atompair_list_ : core::scoring::custom_pair_distance::AtomPairFuncList
• InteractingRotamerExplosion() : protocols::task_operations::InteractingRotamerExplosion
• 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_graph_threads() : protocols::minimization_packing::DisulfideOptimizationMover
• interaction_graph_threads_ : protocols::minimization_packing::DisulfideOptimizationMover
• interaction_radii_squared() : protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• INTERACTION_RADIUS : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• interaction_score_threshold : protocols::constel::NeighTeller
• InteractionEnergyMetric() : core::simple_metrics::metrics::InteractionEnergyMetric
• InteractionGraphBase() : core::pack::interaction_graph::InteractionGraphBase
• InteractionGraphBaseCOP : protocols::pack_daemon::PackDaemon
• InteractionGraphBaseOP : protocols::pack_daemon::PackDaemon
• InteractionGraphSummaryMetric() : protocols::quantum_annealing::InteractionGraphSummaryMetric
• InteractionType : core::scoring::dna::DNA_BasePotential
• InteratomicVarianceMatrix() : protocols::toolbox::InteratomicVarianceMatrix
• InterbondAngleScore() : protocols::frag_picker::scores::InterbondAngleScore
• intercept() : core::scoring::packing::HolesParams , core::sequence::Line
• intercept_ : core::scoring::methods::HRF_MSLabelingEnergy , core::scoring::packing::HolesParams
• intercepts_ : core::scoring::packing::HolesParams
• interchain_env_log_ : protocols::scoring::InterchainPotential
• interchain_pair_log_ : protocols::scoring::InterchainPotential
• interchain_potential_ : protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy
• InterchainEnvEnergy() : protocols::scoring::methods::InterchainEnvEnergy
• InterchainJumpSelector() : core::select::jump_selector::InterchainJumpSelector
• InterchainPairEnergy() : protocols::scoring::methods::InterchainPairEnergy
• InterchainPotential() : protocols::scoring::InterchainPotential
• interchangeability_group() : core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder
• interchangeability_group_ : core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder
• interchangeability_group_generated_by_base_residue_name() : core::chemical::ResidueTypeSetCache
• interchangeability_group_generated_by_base_residue_name_ : core::chemical::ResidueTypeSetCache
• interE : protocols::simple_moves::ThermodynamicData
• interf_distance_ : protocols::hbnet::HBNetStapleInterface
• interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• Interface() : protocols::ligand_docking::ligand_options::Interface , protocols::scoring::Interface
• interface() : protocols::scoring::InterfaceInfo
• interface_ : protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::dna::DnaInterfaceMinMover , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::docking::InterfaceSidechainMinMover , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::rigid::RigidBodyPerturbMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• interface_analyzer_ : protocols::features::InterfaceFeatures
• interface_atoms_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• interface_builder_ : protocols::ligand_docking::MinimizeBackbone
• interface_builder_ct_namer() : protocols::ligand_docking::InterfaceBuilderLoader
• interface_calc() : protocols::anchored_design::AnchorMoversData
• interface_calc_ : protocols::anchored_design::AnchorMoversData
• interface_chi1_ : protocols::seeded_abinitio::SeedSetupMover
• interface_chi2_ : protocols::seeded_abinitio::SeedSetupMover
• interface_data_ : protocols::antibody::AntibodyFeatures
• interface_data_res_ : protocols::antibody::AntibodyFeatures
• interface_ddg_ : protocols::ddg::ddGMover
• INTERFACE_DDG_MUTATION : core::pose::datacache::CacheableDataType
• interface_definition_ : protocols::monte_carlo::MonteCarloInterface
• interface_detection_dis() : protocols::antibody::design::GeneralAntibodyModeler
• interface_dis_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::GeneralAntibodyModeler
• interface_dist_ : protocols::docking::InterfaceSidechainMinMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• interface_distance_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• interface_distance_cutoff() : protocols::task_operations::ProteinInterfaceDesignOperation
• interface_distance_cutoff_ : protocols::calc_taskop_movers::DesignRepackMover , protocols::enzdes::LigInterfaceEnergyFilter , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter , protocols::task_operations::ProteinInterfaceDesignOperation
• interface_exists() : protocols::features::InterfaceFeatures
• interface_from_pose() : protocols::scoring::InterchainPotential
• interface_hbonds : protocols::analysis::InterfaceData
• INTERFACE_INFO : core::pose::datacache::CacheableDataType
• interface_interaction_energy() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• interface_jump_ : protocols::analysis::InterfaceAnalyzerMover
• interface_list_ : protocols::scoring::InterfaceInfo
• interface_motif_score() : protocols::legacy_sewing::scoring::LegacyPartnerMotifScorer , protocols::sewing::scoring::PartnerMotifScorer , protocols::sewing::scoring::SubsetPartnerMotifScorer
• interface_nres : protocols::analysis::InterfaceData , protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• interface_number() : core::conformation::symmetry::SymmetryInfo
• interface_only() : core::scoring::motif::ResPairMotifQuery
• interface_only_ : core::scoring::motif::ResPairMotifQuery
• interface_packer_ : protocols::flexpep_docking::FlexPepDockingProtocol
• interface_radius() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• interface_radius_ : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• interface_res_ : protocols::stepwise::monte_carlo::mover::DeleteMover
• interface_residues : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• interface_set_ : protocols::analysis::InterfaceAnalyzerMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• interface_tf_ : protocols::antibody::design::GeneralAntibodyModeler , protocols::flexpep_docking::FlexPepDockingProtocol
• interface_to_surface_fraction : protocols::analysis::InterfaceData
• interface_trim_radius() : core::scoring::sc::ElectrostaticComplementarityCalculator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric
• interface_trim_radius_ : core::scoring::sc::ElectrostaticComplementarityCalculator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric
• InterfaceAnalyzerMover() : protocols::analysis::InterfaceAnalyzerMover
• InterfaceBindingEnergyDensityFilter() : protocols::simple_ddg::InterfaceBindingEnergyDensityFilter
• InterfaceBuilder() : protocols::ligand_docking::InterfaceBuilder
• InterfaceBuilderLoader() : protocols::ligand_docking::InterfaceBuilderLoader
• InterfaceDdGMover() : protocols::features::InterfaceDdGMover
• InterfaceDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• InterfaceDeltaEnergetics_ : protocols::analysis::InterfaceAnalyzerMover
• InterfaceDeltaEnergeticsCalculator() : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• InterfaceFeatures() : protocols::features::InterfaceFeatures
• InterfaceHbondsFilter() : protocols::simple_filters::InterfaceHbondsFilter
• InterfaceHolesFilter() : protocols::protein_interface_design::filters::InterfaceHolesFilter
• InterfaceHydrophobicResidueContactsFilter() : protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter
• InterfaceInfo() : protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::scoring::InterfaceInfo
• InterfaceNeighborDefinition_ : protocols::analysis::InterfaceAnalyzerMover
• InterfaceNeighborDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
• InterfacePackingFilter() : protocols::matdes::InterfacePackingFilter
• InterfaceRecapitulationMover() : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• interfaces_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo , protocols::features::InterfaceFeatures
• InterfaceSasaDefinition_ : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• InterfaceSasaDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• InterfaceSasaFilter() : protocols::simple_filters::InterfaceSasaFilter
• InterfaceScoreCalculator() : protocols::ligand_docking::InterfaceScoreCalculator
• InterfaceSidechainMinMover() : protocols::docking::InterfaceSidechainMinMover
• InterfaceTaskOperation() : protocols::simple_task_operations::InterfaceTaskOperation
• InterGroupInterfaceByVectorSelector() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• InterGroupNeighborsCalculator() : protocols::pose_metric_calculators::InterGroupNeighborsCalculator
• interhelical_contact() : protocols::hbnet::HBNetStapleInterface
• InterlockAroma() : protocols::flxbb::InterlockAroma
• InterlockingAromaFilter() : protocols::fldsgn::filters::InterlockingAromaFilter
• intermediate_interfaces_ : protocols::antibody::AntibodyFeatures
• intermediate_structs() : protocols::jd2::archive::Batch
• intermediate_structs_ : protocols::jd2::archive::Batch
• intermediate_weights_ : protocols::moves::RampingMover
• intermedrelax() : protocols::comparative_modeling::LoopRelaxMover , protocols::indel::IndelOptimizationMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• intermedrelax_ : protocols::comparative_modeling::LoopRelaxMover , protocols::indel::IndelOptimizationMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• InterModelMotifScorer() : protocols::sewing::scoring::InterModelMotifScorer
• IntermolEnergy() : core::scoring::methods::IntermolEnergy
• internal_allowed_ : core::scoring::packstat::Slice
• internal_coords_need_updating_ : core::kinematics::AtomTree
• internal_cycles_ : protocols::stepwise::monte_carlo::mover::AddMover
• internal_geometry_ : protocols::minimization_packing::MinimalRotamer
• internalize_new_domain_map() : core::scoring::Energies
• InternalMatrix : core::chemical::VDDistanceMatrix
• InternalVector : core::chemical::VDDistanceMatrix
• InternalWorkingResidueParameter() : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• 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_nrchi_values() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• interpolate_on_statistics() : protocols::noesy_assign::PeakCalibrator
• interpolate_property_penalties() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• interpolate_rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• interpolate_too_big() : protocols::noesy_assign::PeakCalibrator
• interpolate_too_small() : protocols::noesy_assign::PeakCalibrator
• interpolated_analytic_etable_evaluation() : core::scoring::etable::Etable
• interpolated_potential_ : core::scoring::rna::data::RNA_DMS_Potential
• interpolator_ : core::scoring::func::SplineFunc
• InterRepeatContactFilter() : protocols::simple_filters::InterRepeatContactFilter
• 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
• intersect_residues() : protocols::vardist_solaccess::VarSolDRotamerDots
• intersects() : protocols::forge::build::Interval
• intersubunit_hbond_energy() : core::scoring::ScoreFunction
• Interval : protocols::fldsgn::BluePrintBDR
• interval() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight
• Interval() : protocols::forge::build::Interval
• interval() : protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• Interval : protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover , protocols::jumping::Interval
• Interval2Interval : protocols::forge::build::BuildManager
• Interval2MoveMap : protocols::forge::build::BuildManager
• Interval2Positions : protocols::forge::build::BuildManager
• interval_ : protocols::checkpoint::Timer , protocols::constraints_additional::COMCoordinateConstraint , protocols::forge::build::Bridge , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• interval_posedump_ : protocols::canonical_sampling::CanonicalSamplingMover
• interval_transitiondump_ : protocols::canonical_sampling::CanonicalSamplingMover
• intervals() : protocols::forge::build::BuildManager
• intervals_ : protocols::forge::constraints::InverseRotamersRCG
• intervals_containing_defined_positions() : protocols::forge::build::BuildManager
• intervals_containing_new_positions() : protocols::forge::build::BuildManager
• intervals_containing_preexisting_positions() : protocols::forge::build::BuildManager
• intervals_containing_undefined_positions() : protocols::forge::build::BuildManager
• intervals_without_valid_original_equivalents() : protocols::forge::build::BuildManager
• intgrp_ : core::chemical::SetInterchangeabilityGroup_String
• intialize_free_and_fixed_energy_terms() : protocols::optimize_weights::IterativeOptEDriver
• intint : protocols::sic_dock::scores::MotifHashRigidScore
• intra_atr_ : protocols::make_rot_lib::RotData
• intra_elec_scale() : core::scoring::FACTSRsdTypeInfo
• intra_elec_scale_ : core::scoring::FACTSRsdTypeInfo
• intra_rep_ : protocols::make_rot_lib::RotData
• intra_residue_constraints_ : core::scoring::constraints::ConstraintSet
• intra_residue_energy() : core::scoring::constraints::Constraints
• intra_segment_requirements_ : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• intra_segment_types_ : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• intra_solv_scale() : core::scoring::FACTSRsdTypeInfo
• intra_solv_scale_ : core::scoring::FACTSRsdTypeInfo
• intrabb_only_ : protocols::matdes::BuildingBlockInterfaceOperation
• IntraClusterIterator : protocols::toolbox::ClusterBase
• IntraDesignTerminusMotifScorer() : protocols::sewing::scoring::IntraDesignTerminusMotifScorer
• intraE : protocols::simple_moves::ThermodynamicData
• IntraRepeatContactFilter() : protocols::simple_filters::IntraRepeatContactFilter
• 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_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_all : core::kinematics::jacobian::ModuleType1::jacobian_struct
• inv_cons : core::kinematics::jacobian::ModuleType1::jacobian_struct
• inv_cov_ : core::scoring::rna::RNA_SuitePotential , core::scoring::rna::TNA_SuitePotential
• inv_die() : core::scoring::FACTSPotential
• inv_die_ : core::scoring::FACTSPotential
• inv_dist6() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• inv_dofs : core::kinematics::jacobian::ModuleType1::jacobian_struct
• inv_dots_ : core::pack::interaction_graph::InvRotamerDots
• inv_neg2_tms_pi_sqrt_pi : core::scoring::magnesium::MgEnergy
• inv_one_minus_xval_at_0p5_ : protocols::moves::InvGeometricFunc
• inv_xval_at_0p5_ : protocols::moves::GeometricFunc
• invalid_ : protocols::jd2::archive::Batch
• INVALIDATE : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent
• invalidate_score_variations() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• invDcnst() : core::scoring::RDC_Rohl
• inverse() : core::kinematics::RT
• inverse_rotamers_ : protocols::forge::constraints::InverseRotamersRCG
• inverse_rotamers_against_residue() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• InverseRotamersRCG() : protocols::forge::constraints::InverseRotamersRCG
• invert() : core::pack::task::residue_selector::ClashBasedShellSelector , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::filters::CompoundFilter , protocols::loops::Loops , protocols::membrane::geometry::Embedding , protocols::membrane::geometry::EmbeddingDef , protocols::task_operations::StoreCompoundTaskMover
• invert_ : core::select::residue_selector::DensityFitResidueSelector , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::filters::CompoundFilter , protocols::filters::IfThenFilter , protocols::task_operations::CrystalContactsOperation , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::SelectByDensityFitOperation , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover
• invert_chains_ : protocols::simple_moves::SwitchChainOrderMover
• invert_direction() : protocols::normalmode::NormalModeRelaxMover
• invert_downstream_ : core::kinematics::Jump
• invert_task_ : protocols::calc_taskop_movers::ConsensusDesignMover
• invert_to_boolmasks() : core::pack::interaction_graph::RotamerDots
• invert_to_compact_array() : core::pack::interaction_graph::DotSphere
• invert_Tsymm() : core::conformation::symmetry::SymmetricConformation
• invert_upstream_ : core::kinematics::Jump
• invert_vector() : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::scoring::RamaPrePro
• inverted_frame_ : core::kinematics::tree::BondedAtom
• InvertJump_ : protocols::symmetry::SymmetrySlider
• invfactor() : core::scoring::BondOrderParser
• InvGeometricFunc() : protocols::moves::InvGeometricFunc
• 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 > , core::scoring::lkball::LK_Ball_BB_BB_E_Invoker , core::scoring::lkball::LK_Ball_BB_SC_E_Invoker , core::scoring::lkball::LK_Ball_RPE_Invoker , core::scoring::lkball::LK_Ball_SC_SC_E_Invoker
• Invoker() : core::scoring::etable::count_pair::Invoker
• involves_current_pose() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• involves_current_pose_ : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• invrot_targets_ : protocols::toolbox::match_enzdes_util::InvrotTree
• invrot_tree_ : protocols::fldsgn::BluePrintBDR , protocols::forge::constraints::InvrotTreeRCG , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• invrot_tree_constraints_ : protocols::toolbox::match_enzdes_util::InvrotTree
• InvRotamerDots() : core::pack::interaction_graph::InvRotamerDots
• InvrotCollector() : protocols::toolbox::match_enzdes_util::InvrotCollector
• invrots() : protocols::toolbox::match_enzdes_util::InvrotCollector
• invrots_ : protocols::toolbox::match_enzdes_util::InvrotCollector
• invrots_and_next_nodes_ : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• invrots_node_ptrs_pair : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• InvrotTarget() : protocols::toolbox::match_enzdes_util::InvrotTarget
• InvrotTree() : protocols::toolbox::match_enzdes_util::InvrotTree
• InvrotTreeNode() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• InvrotTreeNodeBase() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• InvrotTreeRCG() : protocols::forge::constraints::InvrotTreeRCG
• inward_normal_to_plane() : protocols::docking::EllipsoidalRandomizationMover
• INWARDS : core::scoring::dssp::Pairing
• io_stride_ : protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrialCounterObserver
• ion_data_table_ : core::io::nmr::ParamagneticDatabaseHandler
• ion_label_ : core::io::nmr::ParaIon
• ion_type_ : core::scoring::nmr::pre::PREMultiSet
• ionc : core::scoring::APBSConfig
• IonizableResidue() : protocols::simple_moves::IonizableResidue
• ionizables_ : protocols::simple_moves::ReportEffectivePKA
• ionized_restype_ : protocols::simple_moves::IonizableResidue
• ionized_restypes() : protocols::simple_moves::IonizableResidue
• ionq : core::scoring::APBSConfig
• ionr : core::scoring::APBSConfig
• iparam19 : core::scoring::APBSConfig::I_PARAM
• ipca_ : protocols::evaluation::PCA
• ipdb : protocols::simple_filters::ResidueDepthData , protocols::simple_filters::ResidueDepthFrag
• ipos_ : core::fragment::FragID_Iterator
• iptsn_ : core::scoring::SecondaryStructurePotential
• IRCollection() : protocols::motifs::IRCollection
• ires : protocols::simple_filters::ResidueDepthData , protocols::simple_filters::ResidueDepthFrag
• IRmsdFilter() : protocols::protein_interface_design::filters::IRmsdFilter
• irrelevant_jump() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• irun : protocols::mpi_refinement::MethodParams
• is4D() : protocols::noesy_assign::CrossPeak
• is_a_chimaera_ : protocols::sewing::data_storage::SmartSegment
• is_a_neighbor_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• is_a_submotif() : core::pose::full_model_info::FullModelInfo
• is_a_submotif_seed() : core::pose::full_model_info::FullModelInfo
• is_acc_chem_type() : core::scoring::hbonds::HBondTypeManager
• is_acceptor() : core::chemical::AtomType , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup , core::scoring::hbonds::graph::AtomInfo
• IS_ACCEPTOR : core::scoring::hbonds::graph::AtomInfo
• is_acceptor() : core::scoring::hbonds::graph::AtomInfo , protocols::ligand_docking::ga_ligand_dock::AtomProperties , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• is_acceptor_ : core::chemical::AtomType , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• is_acetylated() : core::chemical::carbohydrates::CarbohydrateInfo
• is_acetylated_nterminus() : core::chemical::ResidueType
• is_achiral_backbone() : core::chemical::ResidueTypeBase
• is_achiral_sidechain() : core::chemical::ResidueTypeBase
• is_actcoord() : core::chemical::Atom
• is_actcoord_ : core::chemical::Atom
• is_acyclic() : core::chemical::carbohydrates::CarbohydrateInfo
• is_addable_res() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• is_adduct() : core::chemical::ResidueType
• is_aldose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_all_alpha_aa_or_peptoid() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• is_allowed_residue_type() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• is_allowed_type() : core::scoring::methods::RamaPreProEnergy , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper , protocols::simple_filters::BuriedSurfaceAreaFilter
• is_alpha_aa() : core::chemical::ResidueType
• is_alpha_helical() : protocols::membrane::MPLipidAccessibility
• is_alpha_helical_ : protocols::membrane::MPLipidAccessibility
• 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_any_pdb_empty() : protocols::ddg::ddGMover
• 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_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_archive_rank() : protocols::jd2::archive::MPIArchiveJobDistributor
• is_arg() : core::scoring::methods::ArgCationPiEnergy
• 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::conformation::carbohydrates::GlycanTreeSetObserver , core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver , protocols::denovo_design::components::StructureDataObserver , protocols::moves::PyMOLObserver , protocols::network::UIObserver , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• is_backbone() : core::chemical::Atom , core::scoring::hbonds::graph::AtomInfo
• IS_BACKBONE : core::scoring::hbonds::graph::AtomInfo
• is_backbone() : core::scoring::hbonds::graph::AtomInfo , core::scoring::hbonds::hbtrie::HBAtom , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• is_backbone_ : core::chemical::Atom , core::scoring::hbonds::hbtrie::HBAtom , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• is_backbone_heavyatom() : core::chemical::MutableResidueType
• is_backbone_only_cst() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• is_backward_res_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• is_barrel() : protocols::fldsgn::topology::Sheet
• is_barrel_ : protocols::fldsgn::topology::Sheet
• is_base_paired() : protocols::dna::DNAParameters
• is_base_type() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::ResidueTypeBase
• 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() : protocols::loop_grower::LoopGrower
• is_beta_aa() : core::chemical::ResidueType
• is_beta_aminoacid() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• is_beta_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_bonded() : core::conformation::Conformation , core::conformation::Residue
• is_bonded_values_ : core::scoring::rna::data::RNA_DMS_Potential
• is_branch_point() : core::chemical::ResidueType , core::conformation::Residue
• is_build_stage_enabled_ : protocols::loop_modeler::LoopModeler
• is_bulge() : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• is_bulged() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_bulged_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_buried() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid , core::scoring::rna::RNA_ScoringInfo , protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• is_buried_ : core::scoring::rna::RNA_ScoringInfo
• is_buried_ring() : protocols::pockets::GenPharmacophore
• is_c_terminus_fixed() : protocols::sewing::data_storage::SmartSegment
• is_camelid() : protocols::antibody::Ab_TemplateInfo , protocols::antibody::AntibodyInfo
• is_camelid_ : protocols::antibody::AntibodyInfo , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody_legacy::CDRH3Modeler
• is_cancelled() : protocols::jd2::archive::Batch
• is_cancelled_ : protocols::jd2::archive::Batch
• is_canonical() : core::chemical::ResidueType
• is_canonical_aa() : core::chemical::ResidueType
• is_canonical_beta_nov16_library() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• is_canonical_d_aminoacid() : core::scoring::Ramachandran
• is_canonical_dun02_library_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• is_canonical_nucleic() : core::chemical::ResidueType
• is_canonical_talaris_library() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• is_carbohydrate() : core::chemical::ResidueType , core::conformation::Residue
• is_catalytic_position() : protocols::enzdes::EnzdesBaseProtocol
• is_centroid() : core::conformation::Conformation , core::pose::Pose
• is_centroid_stage_enabled_ : protocols::loop_modeler::LoopModeler
• is_chain_pair_new_ : protocols::peptide_deriver::PeptideDeriverPoseOutputter
• 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_chimaeric() : protocols::sewing::data_storage::SmartSegment
• is_claim() : protocols::environment::claims::EnvClaim
• is_clashing() : core::simple_metrics::per_residue_metrics::PerResidueClashMetric
• is_close() : protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• is_closer_to_tgt() : protocols::constel::OrientCommon
• 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_complete() : protocols::ddg::ddGMover
• is_compliant() : protocols::noesy_assign::CovalentCompliance
• is_conjugatable() : core::chemical::Element
• is_conjugated() : core::chemical::gasteiger::GasteigerAtomTypeData
• is_connect() : core::chemical::ICoorAtomID
• is_connected() : core::conformation::carbohydrates::GlycanTree
• is_conserved() : core::pose::datacache::PositionConservedResiduesStore
• is_constel_valid() : protocols::constel::MasterFilter
• is_continuous() : core::fragment::Frame , core::fragment::NonContinuousFrame , protocols::sewing::data_storage::SmartAssembly
• is_counted() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup , protocols::simple_filters::LongestContinuousApolarSegmentFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter
• is_counted_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• is_covalent() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• is_covalent_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• is_crystal_contact() : protocols::task_operations::CrystalContactsOperation
• is_cstE_ : protocols::enzdes::EnzScoreFilter
• is_cut() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• is_cutpoint() : core::kinematics::FoldTree
• is_cutpoint_ : core::kinematics::FoldTree , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• is_cutpoint_close() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• is_cyclic() : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueType
• is_cyclic_peptide() : protocols::cyclic_peptide::CycpepSymmetryFilter
• is_cyclizable : protocols::peptide_deriver::CyclizedPeptideInfo
• is_d_aa() : core::chemical::ResidueTypeBase
• is_d_aminoacid() : core::scoring::methods::ReferenceEnergy
• is_d_rna() : core::chemical::ResidueTypeBase , core::conformation::Residue
• is_D_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_data_type() : core::io::mmtf::ExtraDataEnumManager
• is_default() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• is_default_ : protocols::kinematic_closure::perturbers::PerturberSet , protocols::loop_modeling::utilities::LoopMoverGroup
• is_deriv_type() : core::scoring::hbonds::HBondTypeManager
• is_designed() : protocols::mean_field::RotMatrix
• is_designed_ : protocols::mean_field::RotMatrix
• is_disulfide() : core::scoring::disulfides::CentroidDisulfidePotential
• is_disulfide_bonded() : core::chemical::ResidueType
• is_DNA() : core::chemical::ResidueTypeBase , core::conformation::Residue
• is_dna() : core::scoring::hbonds::hbtrie::HBAtom
• is_dna_ : core::scoring::hbonds::hbtrie::HBAtom
• is_do_minimize_ : protocols::peptide_deriver::PeptideDeriverFilter
• is_dominant() : protocols::mpi_refinement::MultiObjective
• is_don_chem_type() : core::scoring::hbonds::HBondTypeManager
• is_donor() : core::chemical::AtomType , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup , core::scoring::hbonds::graph::AtomInfo
• IS_DONOR : core::scoring::hbonds::graph::AtomInfo
• is_donor() : core::scoring::hbonds::graph::AtomInfo , protocols::ligand_docking::ga_ligand_dock::AtomProperties , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• is_donor_ : core::chemical::AtomType
• is_dump_best_peptide_pose_ : protocols::peptide_deriver::PeptideDeriverPoseOutputter
• is_dump_cyclic_poses_ : protocols::peptide_deriver::PeptideDeriverFilter , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• is_dump_peptide_pose_ : protocols::peptide_deriver::PeptideDeriverFilter
• is_dump_prepared_pose_ : protocols::peptide_deriver::PeptideDeriverFilter , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• is_dump_report_file_ : protocols::peptide_deriver::PeptideDeriverFilter
• is_edge_file_loaded() : protocols::sewing::hashing::EdgeMapGenerator
• is_edge_file_loaded_ : protocols::sewing::hashing::EdgeMapGenerator
• is_elimination_candidate() : protocols::noesy_assign::CrossPeak
• is_empty() : core::scoring::constraints::ConstraintSet , protocols::loop_grower::LoopPartialSolutionStore , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• is_empty_ : protocols::stepwise::sampler::StepWiseSamplerComb
• is_ensemble_prepacked() : protocols::docking::DockingProtocol
• is_enzyme_not_yet_loaded() : core::enzymes::EnzymeManager
• is_equivalent() : core::kinematics::FoldTree
• is_excluded() : protocols::mpi_refinement::Scheduler
• is_experimental_technique() : core::io::HeaderInformation
• is_extended : protocols::hbnet::HBondNetStruct , protocols::loops::Loop
• is_fail_ : protocols::flexpep_docking::FlexPepDockingProtocol
• is_fake() : core::chemical::Atom , core::chemical::Bond , core::chemical::Element
• is_FAMILYVW() : protocols::simple_filters::BuriedSurfaceAreaFilter
• is_file_ : protocols::canonical_sampling::PatchOperation
• is_finished() : protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• is_finite() : core::scoring::EMapVector
• is_fixed_res_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_fixed_res_input_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• is_flexible() : protocols::enzdes::EnzdesFlexBBProtocol
• is_fold_tree_stale_ : protocols::kinematic_closure::BalancedKicMover
• is_folded() : protocols::noesy_assign::FoldResonance
• is_folded_down() : protocols::noesy_assign::FoldResonance
• is_folded_up() : protocols::noesy_assign::FoldResonance
• is_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• is_forward_res_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• is_freedof() : core::scoring::FACTSRsdTypeInfo
• is_freedof_ : core::scoring::FACTSRsdTypeInfo
• is_frozen_ : protocols::cluster::APCluster
• is_fullatom() : core::conformation::Conformation , core::fragment::rna::FullAtomRNA_Fragments , core::fragment::rna::RNA_Fragments , core::pose::Pose , protocols::rna::denovo::coarse::CoarseRNA_Fragments
• is_fullatom_stage_enabled_ : protocols::loop_modeler::LoopModeler
• is_furanose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_gamma_aa() : core::chemical::ResidueType
• 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_geometry_initialized() : protocols::fldsgn::topology::SS_Base
• is_geometry_initialized_ : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Base
• is_ghost_ : protocols::boinc::BoincCurrentPoseObserver
• is_glob() : core::scoring::saxs::FormFactor
• is_glob_ : protocols::scoring::methods::saxs::PDDFEnergy
• is_glycoside() : core::chemical::carbohydrates::CarbohydrateInfo
• is_glycoside_ : core::chemical::carbohydrates::CarbohydrateInfo
• is_good() : core::sequence::ScoringScheme , protocols::abinitio::Template , protocols::abinitio::Templates
• is_H : protocols::ligand_docking::ga_ligand_dock::AtomProperties
• is_h2o() : core::chemical::AtomType
• is_h2o_ : core::chemical::AtomType
• is_halogen : protocols::ligand_docking::ga_ligand_dock::AtomProperties
• is_haro() : core::chemical::AtomType
• is_hashable() : protocols::sewing::data_storage::SmartSegment
• is_heavy() : core::scoring::packing::PoseBalls
• is_heavy_ : core::scoring::packing::PoseBalls
• is_heavyatom() : core::chemical::AtomType
• is_helical() : core::conformation::membrane::ImplicitLipidInfo
• is_helical_ : core::conformation::membrane::ImplicitLipidInfo
• is_helix() : protocols::features::SecondaryStructureSegmentFeatures
• is_helix_jump() : protocols::abinitio::TemplateJumpSetup
• is_heptose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_het() : core::pose::PDBInfo
• is_hexose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_his() : core::scoring::methods::ArgCationPiEnergy
• is_hit() : core::scoring::mhc_epitope_energy::AlleleMatrix
• is_hybridization_type() : core::scoring::hbonds::HBondTypeManager
• is_hydrogen() : core::chemical::Atom , core::chemical::AtomType , core::scoring::elec::electrie::ElecAtom , core::scoring::etable::etrie::EtableAtom , core::scoring::hbonds::graph::AtomInfo
• IS_HYDROGEN : core::scoring::hbonds::graph::AtomInfo
• is_hydrogen() : core::scoring::hbonds::hbtrie::HBAtom , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::vdwaals::VDWAtom
• is_hydrogen_ : core::scoring::elec::electrie::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_hydrophobic() : protocols::fldsgn::MyAtom
• is_hydrophobic_ : protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity
• is_hydroxyl() : core::scoring::hbonds::graph::AtomInfo
• IS_HYDROXYL : core::scoring::hbonds::graph::AtomInfo
• is_hydroxyl() : core::scoring::hbonds::graph::AtomInfo
• is_identity() : core::id::SequenceMapping
• is_identity_ignore_gaps() : core::id::SequenceMapping
• is_in_Assembly() : protocols::sewing::data_storage::SmartSegment
• is_in_Assembly_ : protocols::sewing::data_storage::SmartSegment
• is_in_between() : core::pose::rna::RNA_SuiteName
• is_in_bin() : core::scoring::bin_transitions::BinTransitionCalculator
• is_in_grid() : core::grid::CartGrid< T > , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridSet , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid
• is_in_helix() : protocols::helical_bundle_predict::HBPHelix , protocols::helical_bundle_predict::HBPHelixAssignments
• is_in_list() : core::scoring::bin_transitions::BinTransitionData , protocols::cyclic_peptide::TryDisulfPermutations , protocols::energy_based_clustering::EnergyBasedClusteringProtocol , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• is_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• is_init() : protocols::toolbox::SamplerPlusPlus
• is_init_ : protocols::rna::denovo::movers::RNP_HighResMover , protocols::toolbox::SamplerPlusPlus
• is_initialized() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , protocols::features::ProteinSilentReport , protocols::fldsgn::BluePrintBDR , protocols::simple_moves::WaterRotsDB
• is_initialized_ : core::pack::task::PackerTask_
• is_interface() : core::scoring::rna::RNA_ScoringInfo , protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• is_interface_ : core::scoring::rna::RNA_ScoringInfo , protocols::scoring::Interface
• is_interface_ddg() : protocols::ddg::ddGMover
• is_interface_residue() : protocols::ligand_docking::InterfaceBuilder
• is_internal() : core::chemical::AtomICoor , core::chemical::ICoorAtomID , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_internal_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_inverted() : core::pack::task::residue_selector::ClashBasedShellSelector
• is_inverted_ : core::pack::task::residue_selector::ClashBasedShellSelector
• is_inverted_virtual_residue() : core::chemical::ResidueType
• is_inwards() : core::scoring::dssp::Pairing
• is_isopeptide_forming_amide_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• is_isopeptide_forming_carbonyl_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• is_it_time() : protocols::moves::PyMOLMover
• is_jump() : core::kinematics::Edge , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , protocols::stepwise::monte_carlo::mover::StepWiseMove
• 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::ResidueTypeBase
• is_l_rna() : core::chemical::ResidueTypeBase , core::conformation::Residue
• is_L_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_ladder() : core::scoring::dssp::StrandPairing
• is_lariat_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• is_lefthanded() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• is_ligand() : core::chemical::ResidueType , core::conformation::Residue , protocols::hbnet::HBondResStruct
• is_ligand_ : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• is_ligand_present() : protocols::flexpep_docking::FlexPepDockingFlags
• is_ligand_terminal() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• is_lipid() : core::chemical::ResidueType
• is_loaded() : core::scoring::methods::dfire::DFIRE_Potential
• is_loop() : protocols::features::HelixCapFeatures , protocols::features::SecondaryStructureSegmentFeatures
• is_loop_residue() : protocols::loops::Loops
• is_lower_terminus() : core::chemical::ResidueType , core::conformation::Residue
• is_lower_terminus_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• 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_medium_base_stack_and_medium_base_pair() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_member() : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::StrandPairing
• is_membrane() : core::chemical::ResidueType , core::conformation::Conformation
• is_mergeable() : core::fragment::Frame
• is_meta_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_metal() : core::chemical::ResidueType , core::conformation::Residue , core::io::NomenclatureManager
• is_metalbinding() : core::chemical::ResidueType , core::conformation::Residue
• is_metapatch() : core::chemical::Patch
• is_metapatch_ : core::chemical::Patch
• is_metapatched() : core::chemical::ResidueTypeBase
• is_metapatched_ : core::chemical::ResidueTypeBase
• is_methylated_cterminus() : core::chemical::ResidueType
• is_mirrored_type() : core::chemical::ResidueType
• is_mixed_mode() : core::conformation::Conformation
• is_movable() : protocols::nonlocal::Chunk
• is_mover : protocols::multistage_rosetta_scripts::mover_or_filter
• is_moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_moving_res_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_multi_trial() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• is_multisegment() : protocols::fold_from_loops::utils::Nub
• is_mutant_calc_complete() : protocols::ddg::ddGMover
• is_N_acetylated() : core::chemical::carbohydrates::CarbohydrateInfo
• is_n_methylated() : core::chemical::ResidueType
• is_N_substituted() : core::scoring::RamaPrePro
• is_n_terminus_fixed() : protocols::sewing::data_storage::SmartSegment
• is_NA() : core::chemical::ResidueType , core::conformation::Residue , core::io::NomenclatureManager
• is_NA_ : core::io::NomenclatureManager
• is_native : protocols::hbnet::HBondNetStruct
• is_native_pairing() : protocols::abinitio::PairingStatistics
• is_native_rotamer_well() : protocols::optimize_weights::PNatRotOptEPositionData
• is_neigh_tree() : protocols::constel::NeighTeller
• is_new_cluster_center_with_working_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• is_ngb : protocols::neighbor::Neighborhood
• is_nonose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_nonpivot_residue() : protocols::kinematic_closure::ClosureProblem
• is_normalization_enabled() : protocols::qsar::scoring_grid::GridSet
• is_normally_connected() : core::scoring::Ramachandran
• is_nub() : core::chemical::RigidDistanceVisitor
• is_nubinitio_tree() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• is_null() : core::scoring::GenTorsionParams , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters , core::scoring::SpringParams
• is_O_acetylated() : core::chemical::carbohydrates::CarbohydrateInfo
• is_observing() : core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo
• is_occupied() : core::pose::rna::VDW_Grid
• is_occupied_ : core::pose::rna::VDW_Grid
• is_octose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_old_canonical_dun02_library() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• is_old_DNA() : core::io::NomenclatureManager
• is_old_DNA_ : core::io::NomenclatureManager
• is_old_individual_suite_cluster() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• is_old_RNA() : core::io::NomenclatureManager
• is_old_RNA_ : core::io::NomenclatureManager
• is_oligourea() : core::chemical::ResidueType
• is_on() : protocols::checkpoint::Timer
• is_on_ : protocols::checkpoint::Timer
• is_open_channel() : protocols::jd2::MpiFileBuffer
• is_optE_type_name() : protocols::optimize_weights::OptEPositionDataFactory
• 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_ortho_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_orthogonal() : core::kinematics::Stub
• is_outwards() : core::scoring::dssp::Pairing
• is_pair() : protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• is_para_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_parallel() : core::scoring::dssp::Pairing , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::StrandPairing
• is_pass_through() : core::chemical::ResidueTypeSetCache
• is_patched() : core::sequence::AnnotatedSequence
• is_pcs_tensor_diagonalized() : core::scoring::nmr::pcs::PCSTensor
• is_pcs_tensor_in_arbitrary_frame() : core::scoring::nmr::pcs::PCSTensor
• is_pcs_tensor_in_pas() : core::scoring::nmr::pcs::PCSTensor
• is_pcs_tensor_reconfigured() : core::scoring::nmr::pcs::PCSTensor
• is_pentose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_peptide() : core::kinematics::Edge
• is_peptoid() : core::chemical::ResidueTypeBase , core::conformation::Residue
• is_phe() : core::scoring::methods::ArgCationPiEnergy
• is_phosphate() : core::chemical::rna::RNA_Info
• is_phosphate_ : core::chemical::rna::RNA_Info
• is_pi() : core::scoring::methods::ArgCationPiEnergy
• is_pivot_res_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• is_pivot_residue() : protocols::kinematic_closure::ClosureProblem
• is_PNA() : core::chemical::ResidueType
• is_point_in_grid() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• is_polar() : core::chemical::ResidueType , core::conformation::Residue
• is_polar_atom() : core::scoring::sasa::SasaMethod
• is_polar_hydrogen() : core::chemical::AtomType
• is_polar_hydrogen_ : core::chemical::AtomType
• is_polarH : protocols::ligand_docking::ga_ligand_dock::AtomProperties , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• is_polymer() : core::chemical::ResidueTypeBase , 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_positive_state() : protocols::multistate_design::SingleState
• is_positive_state_ : protocols::multistate_design::SingleState
• is_post_methylene_meta_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_post_methylene_ortho_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_post_methylene_para_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_pre_methylene_meta_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_pre_methylene_ortho_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_pre_methylene_para_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_pre_methylene_post_methylene_meta_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_pre_methylene_post_methylene_ortho_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_pre_methylene_post_methylene_para_aramid() : core::chemical::ResidueType , core::conformation::Residue
• is_pre_proline() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_pre_proline_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• is_prepend : protocols::stepwise::modeler::rna::sugar::SugarModeling , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_prepend_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::screener::AnchorSugarScreener
• is_prepend_map() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_prepend_map_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_prohibited() : core::chemical::ResidueTypeSetCache
• is_properly_initialized() : protocols::ddg::ddGMover , protocols::simple_moves::ShakeStructureMover
• is_protected() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• is_protected_values_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_protein() : core::chemical::ResidueTypeBase , core::conformation::Residue , core::scoring::hbonds::hbtrie::HBAtom , protocols::hbnet::HBondResStruct
• is_protein_ : core::scoring::hbonds::hbtrie::HBAtom
• is_proton() : protocols::noesy_assign::Resonance
• is_proton_ : protocols::noesy_assign::Resonance
• is_proton_chi() : core::chemical::MutableChiRecord , core::chemical::MutableResidueType , core::chemical::ResidueType
• is_proton_chi_ : core::chemical::MutableChiRecord , core::chemical::ResidueType
• is_pseudo_bonded() : core::conformation::Residue
• is_purine() : core::chemical::ResidueType , core::conformation::Residue
• is_pyramidal() : protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper
• is_pyramidal_ : protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper
• is_pyranose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_pyrimidine() : core::chemical::ResidueType , core::conformation::Residue
• is_qsar_map_attached() : protocols::qsar::scoring_grid::GridSet
• is_quenched() : protocols::carbohydrates::GlycanTreeModeler
• is_r_peptoid() : core::chemical::ResidueTypeBase
• is_random_ : protocols::mpi_refinement::Scheduler
• is_rdc_tensor_in_arbitrary_frame() : core::scoring::nmr::rdc::RDCTensor
• is_rdc_tensor_in_pas() : core::scoring::nmr::rdc::RDCTensor
• is_reducing_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_reference_xyz_setup_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• is_registered() : protocols::environment::Environment
• is_relevant_neighbor() : core::scoring::nmr::NMRDummySpinlabelAtom , core::scoring::nmr::VoxelGridPoint , protocols::nmr::pcs::AtomGridPoint
• is_remodelable() : protocols::enzdes::EnzdesFlexBBProtocol
• is_report_gzip_ : protocols::peptide_deriver::PeptideDeriverFilter
• is_representative_resonance() : protocols::noesy_assign::FloatingResonance
• is_representative_resonance_ : protocols::noesy_assign::FloatingResonance
• is_repulsive() : core::chemical::AtomType , core::chemical::ResidueType , core::conformation::Residue
• is_residue_allowed() : protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• is_residue_ignored_in_rms() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• is_residue_in_grid() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• is_residue_in_tree() : core::conformation::carbohydrates::GlycanTreeSet
• is_residue_type_recognized() : core::io::pose_from_sfr::PoseFromSFRBuilder
• is_reversible() : core::scoring::motif::ResPairMotif
• is_ring_atom() : core::chemical::ResidueType
• is_rmoi_hbonded() : protocols::constel::HBondCommon
• is_RNA() : core::chemical::ResidueTypeBase , core::conformation::Residue
• is_rna_and_protein() : core::import_pose::RNA_DeNovoParameters
• is_rna_and_protein_ : core::import_pose::RNA_DeNovoParameters , protocols::rna::denovo::RNA_FragmentMonteCarlo
• is_RNA_base() : core::chemical::rna::RNA_Info
• is_rna_base() : core::scoring::rna::StackElecEnergy
• is_RNA_base_ : core::chemical::rna::RNA_Info
• is_RNA_base_atom() : core::chemical::rna::RNA_Info
• is_RNA_bulge() : core::scoring::rna::RNA_BulgeEnergy
• is_root() : core::kinematics::FoldTree
• is_rotamer_terminal() : core::scoring::trie::TrieNode< AT, CPDATA >
• is_s_peptoid() : core::chemical::ResidueTypeBase
• is_satisfied() : protocols::constel::FilterByAmphetamine , protocols::constel::FilterByHistamine , protocols::constel::FilterByIndoleCOO , protocols::constel::FilterByProxTerm , protocols::constel::FilterByTryptamine
• is_sc() : core::scoring::hbonds::hbtrie::HBCPData
• is_sc_ : core::scoring::hbonds::hbtrie::HBCPData
• is_score_precomputed() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_score_precomputed_ : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_score_type() : core::scoring::ScoreTypeManager
• is_score_type_line() : core::io::silent::SilentFileData
• is_scratch_res_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• is_selection_initialized() : core::select::util::SelectResiduesByLayer
• is_selection_initialized_ : core::select::util::SelectResiduesByLayer
• is_septanose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_seq_sep_type() : core::scoring::hbonds::HBondTypeManager
• is_set_s_kk() : protocols::cluster::DataPoint
• is_setup_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• is_sibling_sugar_rotamer_pose() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• is_sidechain_amine() : core::chemical::ResidueType
• is_sidechain_thiol() : core::chemical::ResidueType
• is_similar_aa() : core::conformation::Residue
• is_similar_rotamer() : core::conformation::Residue
• is_simple_full_length_job_params() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_simple_full_length_job_params_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_simple_tree() : core::kinematics::FoldTree
• is_single() : core::kinematics::TreeVizBuilder
• is_single_precision() : core::io::silent::ProteinSilentStruct_Template< T >
• is_skip_zero_isc_ : protocols::peptide_deriver::PeptideDeriverFilter
• is_sliced_res_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• is_solution_trivial() : protocols::kinematic_closure::BalancedKicMover
• is_solvent() : core::chemical::ResidueType , protocols::hbnet::HBondResStruct
• is_sparis_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• is_sri() : core::chemical::ResidueType , core::conformation::Residue
• is_start_zero_score() : protocols::jd2::archive::NormalizedEvaluatedArchive
• is_started_ : protocols::jobdist::BaseJobDistributor
• is_strong_base_stack() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_sub_residues() : protocols::hbnet::HBNet
• is_sugar() : core::io::NomenclatureManager
• is_supported_restype() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• 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_symmetric_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• is_symmetric_partner_of() : protocols::noesy_assign::PeakAssignment
• is_tensor_diagonalized() : core::scoring::nmr::rdc::RDCTensor
• is_tensor_reconfigured() : core::scoring::nmr::rdc::RDCTensor
• is_term_ : core::scoring::trie::TrieNode< AT, CPDATA >
• is_terminal() : protocols::loops::Loop
• is_terminal_res_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_terminus() : core::chemical::ResidueType , core::conformation::Residue , protocols::cyclic_peptide::RamaMutationSelector
• is_tetrose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_there_contact() : protocols::docking::DockingSlideIntoContact
• is_TNA() : core::chemical::ResidueType , core::conformation::Residue
• is_TNA_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• is_top() : protocols::dna::DnaChains
• is_torsion_exists() : core::pose::rna::RNA_IdealCoord
• is_TP3() : core::chemical::ResidueType
• is_triazolemer() : core::chemical::ResidueType , core::conformation::Residue
• is_trimmed_loops_ : protocols::flexpep_docking::FlexPepDockingProtocol
• is_triose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_trp() : core::scoring::methods::ArgCationPiEnergy
• is_tyr() : core::scoring::methods::ArgCationPiEnergy
• is_ulose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_under_memory_limit() : protocols::wum::WorkUnitQueue
• is_unsat() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• is_up_to_date_ : protocols::frag_picker::scores::AdaptiveScoreHistogram
• 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 , core::scoring::PolymerBondedEnergyContainer , protocols::jumping::JumpSample , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::noesy_assign::FragsToAtomDist::DistanceRecord , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate
• is_valid_chunk() : protocols::frag_picker::FragmentPicker
• is_valid_modification_affix() : core::chemical::carbohydrates::CarbohydrateInfoManager
• is_valid_quota_pool_name() : protocols::frag_picker::quota::QuotaConfig
• is_valid_record_type() : core::io::pdb::RecordCollection
• is_valid_ring_affix() : core::chemical::carbohydrates::CarbohydrateInfoManager
• is_valid_sugar_code() : core::chemical::carbohydrates::CarbohydrateInfoManager
• is_variant_type() : core::chemical::ResidueProperties
• is_VDW_screen_bin_setup_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• is_virt_sample_sugar_tag() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• is_virtual() : core::chemical::Atom , core::chemical::AtomType , core::chemical::ResidueType , core::chemical::rna::RNA_Info , core::conformation::Residue , core::conformation::symmetry::SymmetryInfo
• is_virtual_ : core::chemical::rna::RNA_Info
• is_virtual_base_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_virtual_residue() : core::chemical::ResidueType , core::conformation::Residue
• is_virtualizable_by_packer() : core::chemical::ResidueType
• is_vital() : protocols::sewing::data_storage::SmartSegment
• is_vital_ : protocols::sewing::data_storage::SmartSegment
• is_VRT1() : core::chemical::ResidueType
• is_wat() : core::scoring::elec::electrie::ElecAtom , core::scoring::etable::etrie::EtableAtom , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::vdwaals::VDWAtom
• is_wat_ : core::scoring::elec::electrie::ElecAtom , core::scoring::etable::etrie::EtableAtom , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::vdwaals::VDWAtom
• is_water() : core::chemical::ResidueType , core::conformation::Residue
• is_weight_type() : core::scoring::hbonds::HBondTypeManager
• is_within_radius() : core::scoring::sc::ElectrostaticComplementarityCalculator
• is_worker_running() : protocols::boinc::Boinc
• is_working_cutpoint_closed() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• is_working_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_working_res_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_wt_calc_complete() : protocols::ddg::ddGMover
• isAcceptor() : protocols::sparta::PDB
• isbb() : core::scoring::elec::electrie::ElecAtom
• isbb_ : core::scoring::elec::electrie::ElecAtom
• IsBondedToAHalogen() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• IsBondInRing() : core::chemical::Bond
• IsBondOrderKnown() : core::chemical::Bond
• isbound : core::scoring::atomic_depth::volumepixel
• isch_ : protocols::mpi_refinement::Scheduler
• isClose() : protocols::pockets::CCluster , protocols::pockets::PCluster
• isCompound() : protocols::rbsegment_relax::RBSegment
• isDeepTargetPocketPoint() : protocols::pockets::PocketGrid
• isDesignable : protocols::forge::remodel::LineObject
• isdone : core::scoring::atomic_depth::volumepixel
• isDonor() : protocols::sparta::PDB
• isEmpty() : core::grid::CartGrid< T > , protocols::rbsegment_relax::RBSegment
• isep_residue_ : protocols::fldsgn::NcontactsCalculator
• isFiberDataLoaded() : core::scoring::fiber_diffraction::FiberDiffraction
• isFullyOccupied() : core::grid::CartGrid< T >
• isGenericRB() : protocols::rbsegment_relax::RBSegment
• isHelix() : protocols::rbsegment_relax::RBSegment
• isHet : core::io::AtomInformation , core::pose::PDBInfo::AtomRecord
• isInContact() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• isLoaded : core::scoring::fiber_diffraction::FiberDiffraction
• isLoaded_ : core::scoring::electron_density::ElectronDensity
• IsMainAtomPredicate() : core::scoring::IsMainAtomPredicate
• isMapLoaded() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• isneigh() : protocols::constel::NeighTeller
• isolate() : protocols::sewing::data_storage::SmartSegment
• isometry() : core::chemical::Bond
• isometry_ : core::chemical::Bond
• IsProteinCAPredicate() : core::scoring::IsProteinCAPredicate
• isProteinPoint() : protocols::pockets::PocketGrid
• IsRelevantItem() : core::scoring::nmr::NMRDummySpinlabelVoxelGrid , protocols::nmr::pcs::AtomGrid
• IsSameItem() : core::scoring::nmr::NMRDummySpinlabelVoxelGrid , protocols::nmr::pcs::AtomGrid
• isSheet() : protocols::rbsegment_relax::RBSegment
• isSimple() : protocols::rbsegment_relax::RBSegment
• isSolventExposed() : protocols::pockets::CCluster , protocols::pockets::PCluster
• isSSBonded() : protocols::sparta::PDB
• issue_passport() : core::environment::EnvCore
• isSurfacePoint() : protocols::pockets::PocketGrid
• isTarget() : protocols::pockets::CCluster , protocols::pockets::PCluster
• isTargetPocketPoint() : protocols::pockets::PocketGrid
• istart : protocols::mpi_refinement::MethodParams
• istart_ : protocols::simple_moves::PeriodicBoxMover
• isTooSmall() : protocols::pockets::PocketGrid
• istruct_ : protocols::ligand_docking::ga_ligand_dock::LigandAligner
• IsUnsaturated() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• isVarFloat() : protocols::sparta::GDB
• isVarInt() : protocols::sparta::GDB
• isVarString() : protocols::sparta::GDB
• 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 , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• Item() : protocols::simple_moves::LoggedFragmentMover::Item
• iter() : protocols::mpi_refinement::Scheduler
• iter64_ : protocols::match::VoxelSetIterator
• iter_ : protocols::mpi_refinement::Scheduler
• iter_begin() : core::conformation::PseudoBondCollection
• iter_collect_begin_ : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• iter_end() : core::conformation::PseudoBondCollection
• iterate() : protocols::frag_picker::ContactCounts
• iterate_bump_selector() : core::pack::rotamer_set::BumpSelector
• iterate_checkpoint_count() : protocols::boinc::Boinc
• iterate_neighbor() : protocols::frag_picker::ContactCounts
• iterate_over_basis_pairs() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::hashing::Hasher
• iterate_tensor_weights() : core::scoring::ResidualDipolarCoupling
• IteratedConvergenceMover() : protocols::moves::IteratedConvergenceMover
• iteration : protocols::canonical_sampling::DbTrajectoryRecorder::Frame , protocols::monte_carlo::AcceptedScores , protocols::trajectory::DbTrajectoryWriter::Frame , protocols::vip::VIP_Mover
• iteration_ : protocols::kinematic_closure::perturbers::LogFilePerturber , protocols::monte_carlo::AcceptedScores , protocols::trajectory::DbTrajectoryWriter , protocols::vip::VIP_Mover
• iteration_counter_ : protocols::loop_modeling::refiners::RepackingRefiner
• iterations() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• iterations_ : protocols::abinitio::abscript::AbscriptMover::StageTracker , protocols::denovo_design::movers::BridgeChainsMover , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::moves::CyclicMover , protocols::rna::movers::RNAIdealizeMover
• iterations_per_phase_ : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• IterationStage : protocols::abinitio::IterativeBase
• IterativeAbrelax() : protocols::abinitio::IterativeAbrelax
• IterativeBase() : protocols::abinitio::IterativeBase
• IterativeCentroid() : protocols::abinitio::IterativeCentroid
• IterativeFullatom() : protocols::abinitio::IterativeFullatom
• iteratively_correct_energy_tensor() : core::chemical::mainchain_potential::MainchainScoreTable
• IterativeOptEDriver() : protocols::optimize_weights::IterativeOptEDriver
• IterativeVectorExpression() : protocols::pack_daemon::IterativeVectorExpression
• iterator : core::conformation::Conformation , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::iterator , core::kinematics::FoldTree , core::optimization::MinimizerMap , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pose::Pose , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector , protocols::abinitio::abscript::ResidueChunkSelection , protocols::constraint_generator::ConstraintsMap , protocols::filters::CompoundFilter , protocols::hotspot_hashing::HotspotStubSet , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::loops::Loops , protocols::mean_field::jagged_array< T, A >
• Iterator : protocols::mean_field::jagged_array< T, A >
• iterator : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::rosetta_scripts::ParsedProtocol , protocols::splice::ResidueBBDofs , protocols::wum::SilentStructStore , protocols::wum::WorkUnitManager , protocols::wum::WorkUnitQueue
• iterator_category : core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::RT , core::kinematics::tree::Atom , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• itoa() : protocols::sparta::ANN
• itterative() : protocols::task_operations::DatabaseThread
• itterative_ : protocols::task_operations::DatabaseThread
• iupac_map() : core::io::NomenclatureManager
• ivm() : protocols::toolbox::InteratomicVarianceMatrix
• ivm_ : protocols::toolbox::InteratomicVarianceMatrix
• IVs : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• ix : core::scoring::atomic_depth::voxel2 , core::scoring::atomic_depth::voxel
• iy : core::scoring::atomic_depth::voxel2 , core::scoring::atomic_depth::voxel
• iz : core::scoring::atomic_depth::voxel2 , core::scoring::atomic_depth::voxel