- c -

• C() : core::pose::CrystInfo , core::scoring::BB_Pos , core::scoring::electron_density::OneGaussianScattering
• c0() : core::scoring::FACTSRsdTypeInfo
• c1() : core::scoring::FACTSRsdTypeInfo
• c1prime_atom_index() : core::chemical::rna::RNA_ResidueType
• c2() : core::scoring::FACTSRsdTypeInfo
• c2prime_atom_index() : core::chemical::rna::RNA_ResidueType
• c3() : core::scoring::FACTSRsdTypeInfo
• c4prime_atom_index() : core::chemical::rna::RNA_ResidueType
• c_alpha_index() : core::scoring::disulfides::DisulfideAtomIndices
• c_beta_index() : core::scoring::disulfides::DisulfideAtomIndices
• CA() : core::scoring::BB_Pos
• ca_cprev_n_h_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• ca_nnext_c_o_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• CA_rmsd() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct
• CaCbCb_Angle_Func() : core::scoring::disulfides::CaCbCb_Angle_Func
• CaCbCbCa_Dihedral_Func() : core::scoring::disulfides::CaCbCbCa_Dihedral_Func
• cache() : core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::Frame
• CacheableAtomID_MapVector() : core::id::CacheableAtomID_MapVector
• CacheableObserver() : core::pose::datacache::CacheableObserver
• CacheablePoseRawPtr() : core::pose::datacache::CacheablePoseRawPtr
• CacheableSequenceProfile() : core::sequence::CacheableSequenceProfile
• CacheWrapper() : core::fragment::CacheWrapper< T, XCacheUnit >
• cal_delta_internal_coordinates() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• cal_delta_internal_coordinates_squared() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• cal_distance() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• cal_distance_squared() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• Calc() : core::scoring::sc::MolecularSurfaceCalculator , core::scoring::sc::ShapeComplementarityCalculator
• calc_atom_masks() : core::scoring::sasa::LeGrandSasa
• calc_cosineang() : core::scoring::methods::GoapEnergy
• calc_deltaEpd() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• calc_dipscore() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_energy() : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• calc_etable_value() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• calc_kl_divergence() : core::scoring::func::MixtureFunc
• calc_ordermatrix() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_orderparam() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_penalty_vec() : core::scoring::constraints::FabConstraint
• calc_per_res_sasas() : core::scoring::sasa::SasaCalc
• calc_phi() : core::scoring::methods::GoapEnergy
• calc_rms_res() : core::pose::full_model_info::FullModelInfo
• calc_rot_freq() : core::pack::annealer::SimAnnealerBase
• CalcDotsForAllAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• CalcDotsForAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• CalcNeighborDistance() : core::scoring::sc::ShapeComplementarityCalculator
• CalcNeighborDistanceFindClosestNeighbor() : core::scoring::sc::ShapeComplementarityCalculator
• calcRhoC() : core::scoring::electron_density::ElectronDensity
• CalcSc() : core::scoring::sc::ShapeComplementarityCalculator
• calculate() : core::scoring::sasa::LeGrandSasa , core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• calculate_alt_state_hpatch_score() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculate_amount_total_hydrophobic_ASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• calculate_contact_order() : core::scoring::methods::ContactOrderEnergy
• calculate_derivatives_for_atoms_and_pseudo_base_atoms() : core::scoring::methods::LK_hack
• calculate_derivatives_for_residue_pair() : core::scoring::methods::LK_hack
• calculate_dipoles() : core::scoring::methods::GoapEnergy
• calculate_energy() : core::scoring::rna::data::RNA_ChemicalMappingEnergy
• calculate_feature_vector() : core::scoring::methods::ProQ_Energy
• calculate_feature_vector_proq2() : core::scoring::methods::ProQ_Energy
• calculate_GBpair_exact() : core::scoring::FACTSPotential
• calculate_GBpair_fast() : core::scoring::FACTSPotential
• calculate_GBpair_v1trunk() : core::scoring::FACTSPotential
• calculate_hpatch_deltaE() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculate_hydrogen_atom_reach() : core::scoring::etable::Etable
• calculate_hydrogen_interaction_cutoff() : core::scoring::vdwaals::VDW_Energy
• calculate_index2cart() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• calculate_interres() : core::scoring::etable::BaseEtableEnergy< Derived >
• calculate_intra_xover4() : core::scoring::etable::BaseEtableEnergy< Derived >
• calculate_intrares() : core::scoring::etable::BaseEtableEnergy< Derived >
• calculate_lk_ball_atom_energies() : core::scoring::methods::LK_BallEnergy
• calculate_lk_ball_atom_energies_cp() : core::scoring::methods::LK_BallEnergy
• calculate_lk_desolvation_of_single_atom_by_residue() : core::scoring::methods::LK_BallEnergy
• calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair() : core::scoring::methods::LK_BallEnergy
• calculate_map() : core::sequence::AnnotatedSequence
• calculate_nblist_distance_thresholds() : core::scoring::etable::Etable
• calculate_normal_disbins() : core::scoring::etable::Etable
• calculate_num_rotamers_in_subtree() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• calculate_orbital_icoor() : core::chemical::orbitals::AssignOrbitals
• calculate_orientation_vectors_and_pseudo_base_atoms() : core::scoring::methods::LK_hack
• calculate_PD_deltaE_for_substitution() : core::pack::interaction_graph::HPatchNode< V, E, G >
• calculate_per_position_scores() : core::sequence::SequenceAlignment
• calculate_rg_score() : core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy
• calculate_score_sum_of_pairs() : core::sequence::SequenceAlignment
• calculate_stability_metric() : core::chemical::gasteiger::GasteigerAtomTypeData
• calculate_subtree_containing_radii() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• calculate_total_cst_score() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• calculated() : core::scoring::CenListInfo , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::rna::RNA_ScoringInfo , core::scoring::SigmoidWeightedCenList< T >
• calculateDensityMap() : core::scoring::cryst::PhenixInterface
• calculateZ() : core::scoring::methods::ProQ_Energy
• CalculatorFactory() : core::pose::metrics::CalculatorFactory
• came_from() : core::sequence::Cell
• can_pair() : core::chemical::AutomorphismIterator
• carbohydrate_info() : core::chemical::ResidueType , core::conformation::Residue
• CarbohydrateInfo() : core::chemical::carbohydrates::CarbohydrateInfo
• CarbonHBondEnergy() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• CarbonHBondPotential() : core::scoring::carbon_hbonds::CarbonHBondPotential
• careful_base_pair_classifier() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• carry_out_filtering() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• cart2frac() : core::scoring::electron_density::ElectronDensity
• cart2idx() : core::scoring::electron_density::ElectronDensity , core::scoring::PoissonBoltzmannPotential
• cart_size() : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• CartesianBondedEnergy() : core::scoring::methods::CartesianBondedEnergy
• CartesianMinimizer() : core::optimization::CartesianMinimizer
• CartesianMinimizerMap() : core::optimization::CartesianMinimizerMap
• CartesianMultifunc() : core::optimization::CartesianMultifunc
• CartGrid() : core::grid::CartGrid< T >
• CartSCMinMinimizerMap() : core::pack::scmin::CartSCMinMinimizerMap
• CartSCMinMultifunc() : core::pack::scmin::CartSCMinMultifunc
• catalog() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• CavityBall() : core::scoring::packstat::CavityBall
• CB() : core::scoring::BB_Pos
• CB_Angle_Func() : core::scoring::disulfides::CB_Angle_Func
• cb_dist_cut() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• Cb_Distance_Func() : core::scoring::disulfides::Cb_Distance_Func
• CBSG_Dihedral_Func() : core::scoring::disulfides::CBSG_Dihedral_Func
• cd_1b_types() : core::scoring::ScoreFunction
• cd_2b_begin() : core::scoring::ScoreFunction
• cd_2b_end() : core::scoring::ScoreFunction
• cd_2b_intrares_begin() : core::scoring::ScoreFunction
• cd_2b_intrares_end() : core::scoring::ScoreFunction
• cd_2b_types() : core::scoring::ScoreFunction
• cd_lr_2b_methods_begin() : core::scoring::ScoreFunction
• cd_lr_2b_methods_end() : core::scoring::ScoreFunction
• cd_lr_2b_types() : core::scoring::ScoreFunction
• cdf_for_aa() : core::scoring::Ramachandran
• cdf_for_aa_for_torsion_bin() : core::scoring::Ramachandran
• Cell() : core::sequence::Cell
• cen_dist10_pad() : core::scoring::membrane::MembraneData
• cen_dist10_pad_hinv() : core::scoring::membrane::MembraneData
• cen_dist10_pad_minus() : core::scoring::membrane::MembraneData
• cen_dist10_pad_plus() : core::scoring::membrane::MembraneData
• cen_dist12_pad() : core::scoring::membrane::MembraneData
• cen_dist12_pad_hinv() : core::scoring::membrane::MembraneData
• cen_dist12_pad_minus() : core::scoring::membrane::MembraneData
• cen_dist12_pad_plus() : core::scoring::membrane::MembraneData
• cen_dist5_pad() : core::scoring::membrane::MembraneData
• cen_dist5_pad_hinv() : core::scoring::membrane::MembraneData
• cen_dist5_pad_minus() : core::scoring::membrane::MembraneData
• cen_dist5_pad_plus() : core::scoring::membrane::MembraneData
• cen_dist6_pad() : core::scoring::membrane::MembraneData
• cen_dist6_pad_hinv() : core::scoring::membrane::MembraneData
• cen_dist6_pad_plus() : core::scoring::membrane::MembraneData
• cen_dist7_pad() : core::scoring::membrane::MembraneData
• cen_dist7_pad_hinv() : core::scoring::membrane::MembraneData
• cen_dist7_pad_minus() : core::scoring::membrane::MembraneData
• cen_dist7_pad_plus() : core::scoring::membrane::MembraneData
• Cen_Distance_Func() : core::scoring::disulfides::Cen_Distance_Func
• CenHBEnergy() : core::scoring::methods::CenHBEnergy
• CenHBPotential() : core::scoring::CenHBPotential
• cenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• CenListInfo() : core::scoring::CenListInfo
• CenPairEnergy() : core::scoring::methods::CenPairEnergy
• CenRotDunEnergy() : core::pack::dunbrack::cenrot::CenRotDunEnergy
• CenRotEnvEnergy() : core::scoring::methods::CenRotEnvEnergy
• CenRotEnvPairPotential() : core::scoring::CenRotEnvPairPotential
• CenRotPairEnergy() : core::scoring::methods::CenRotPairEnergy
• center() : core::conformation::membrane::Span , core::conformation::UltraLightResidue , core::id::NamedStubID , core::id::StubID , core::kinematics::Stub , core::pose::Pose , core::scoring::MembraneEmbed , core::scoring::packstat::PackingScore
• central_atoms_to_score() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• centroid() : core::import_pose::ImportPoseOptions
• CentroidDisulfideEnergy() : core::scoring::disulfides::CentroidDisulfideEnergy
• CentroidDisulfideEnergyComponents() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• CentroidDisulfideEnergyContainer() : core::scoring::disulfides::CentroidDisulfideEnergyContainer
• CentroidDisulfideNeighborConstIterator() : core::scoring::disulfides::CentroidDisulfideNeighborConstIterator
• CentroidDisulfideNeighborIterator() : core::scoring::disulfides::CentroidDisulfideNeighborIterator
• CentroidDisulfidePotential() : core::scoring::disulfides::CentroidDisulfidePotential
• CentroidRotamerSampleData() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• chain() : core::conformation::Residue , core::fragment::AnnotatedFragData , core::fragment::FragData , core::pack::task::operation::ChainIs , core::pose::PDBInfo , core::pose::Pose
• chain_begin() : core::conformation::Conformation
• chain_end() : core::conformation::Conformation
• chain_endings() : core::conformation::Conformation , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_endings_str() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_letter_to_number() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain_sequence() : core::pose::Pose
• chain_strings() : core::pack::task::residue_selector::ChainSelector
• ChainbreakEnergy() : core::scoring::methods::ChainbreakEnergy
• ChainIs() : core::pack::task::operation::ChainIs
• ChainIsnt() : core::pack::task::operation::ChainIsnt
• ChainPos() : core::pack::task::operation::ResiduePDBIndexIs::ChainPos
• chains_from_termini() : core::conformation::Conformation
• chains_in_full_model() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• chains_whose_residues_are_separate_chemical_entities() : core::io::pdb::FileDataOptions
• ChainSelector() : core::pack::task::residue_selector::ChainSelector
• changed() : core::scoring::FACTSResidueInfo
• charge() : core::chemical::Atom , core::scoring::elec::ElecAtom
• charged() : core::scoring::FACTSRsdTypeInfo
• CharmmPeriodicFunc() : core::scoring::func::CharmmPeriodicFunc
• check_annotation() : core::io::rna::RDAT
• check_annotations() : core::io::rna::RDAT
• check_atom_numbers_for_backbone_oxygens() : core::scoring::rna::RNA_LowResolutionPotential
• check_atomset_compatibility() : core::coarse::CoarseEtable
• check_base_base_OK() : core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• check_bounds() : core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::motif::MotifHash
• check_calculator_exists() : core::pose::metrics::CalculatorFactory
• check_chbonded() : core::scoring::rna::data::RNA_DMS_Potential
• check_clear_for_stacking() : core::scoring::rna::RNA_LowResolutionPotential
• check_disjoint() : core::scoring::loop_graph::LoopGraph
• check_domain_map() : core::pose::copydofs::CopyDofs , core::scoring::NeighborList
• check_edges_for_atom_info() : core::kinematics::FoldTree
• check_fold_tree() : core::kinematics::FoldTree
• check_for_base_neighbor() : core::scoring::rna::RNA_LowResolutionPotential
• check_for_unexpected_cutpoints() : core::scoring::loop_graph::LoopGraph
• check_forming_base_pair() : core::scoring::rna::RNA_LowResolutionPotential
• check_hairpin() : core::scoring::SS_Killhairpins_Info
• check_hbonded() : core::scoring::rna::data::RNA_DMS_Potential
• check_if_residues_are_Ctermini() : core::io::pdb::FileDataOptions
• check_if_residues_are_Ntermini() : core::io::pdb::FileDataOptions
• check_if_rna_from_sequence_line() : core::io::silent::SilentFileData
• check_internals_() : core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile
• check_intra_residue() : core::scoring::rna::RNA_TorsionPotential
• check_lig_code() : core::scoring::motif::ResPairMotif
• check_loop_cycles_are_disjoint() : core::scoring::loop_graph::LoopGraph
• check_membrane_fold_tree() : core::conformation::membrane::MembraneInfo
• check_methods() : core::scoring::ScoreFunction
• check_methods_in_right_order() : core::scoring::ScoreFunction
• check_order() : core::kinematics::FoldTree
• check_path_distance() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• check_pdb_code() : core::scoring::motif::ResPairMotif
• check_pleat() : core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet
• check_rama() : core::util::ABEGO , core::util::ABEGOManager
• check_rama2() : core::util::ABEGO
• check_rdat() : core::io::rna::RDAT
• check_residue_records_size() : core::pose::PDBInfo
• check_sequence_seqpos() : core::io::rna::RDAT
• check_setup() : core::optimization::AtomTreeMinimizer
• check_spanning() : core::scoring::MembranePotential
• check_sugar_atom() : core::scoring::rna::data::RNA_DataBackboneEnergy
• check_topology() : core::kinematics::FoldTree
• check_valid_membrane() : core::conformation::Conformation
• CheckAtomCollision2() : core::scoring::sc::MolecularSurfaceCalculator
• CheckPointCollision() : core::scoring::sc::MolecularSurfaceCalculator
• CheckProbeCollision() : core::scoring::sc::MolecularSurfaceCalculator
• ChemicalManager() : core::chemical::ChemicalManager
• ChemicalShiftAnisotropy() : core::scoring::ChemicalShiftAnisotropy
• ChemicalShiftAnisotropyEnergy() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• ChemicalShiftData() : core::scoring::rna::chemical_shift::ChemicalShiftData
• ChemicalShiftScoringScheme() : core::sequence::ChemicalShiftScoringScheme
• ChemicalShiftSequence() : core::sequence::ChemicalShiftSequence
• ChemicalShiftSequenceCreator() : core::sequence::ChemicalShiftSequenceCreator
• chi() : core::conformation::Residue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::task::operation::RotamerExplosion , core::pose::Pose
• chi1() : core::scoring::motif::ResPairMotif , core::scoring::motif::Xfres
• chi11() : core::scoring::motif::ResPairMotif
• chi12() : core::scoring::motif::ResPairMotif
• chi13() : core::scoring::motif::ResPairMotif
• chi14() : core::scoring::motif::ResPairMotif
• chi2() : core::scoring::motif::ResPairMotif , core::scoring::motif::Xfres
• chi21() : core::scoring::motif::ResPairMotif
• chi22() : core::scoring::motif::ResPairMotif
• chi23() : core::scoring::motif::ResPairMotif
• chi24() : core::scoring::motif::ResPairMotif
• chi3() : core::scoring::motif::Xfres
• chi4() : core::scoring::motif::Xfres
• chi4E() : core::scoring::methods::ProClosureEnergy
• chi_2_proton_chi() : core::chemical::ResidueType
• chi_atom_vds() : core::chemical::ResidueType
• chi_atoms() : core::chemical::ResidueType , core::conformation::Residue
• chi_clones() : core::conformation::symmetry::SymmetryInfo
• chi_follows() : core::conformation::symmetry::SymmetryInfo
• chi_is_independent() : core::conformation::symmetry::SymmetryInfo
• chi_is_nonrotameric() : core::pack::dunbrack::DunbrackRotamerSampleData
• chi_mean() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_north_anti() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_north_syn() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_number_pseudoalpha() : core::chemical::rna::RNA_ResidueType
• chi_number_pseudobeta() : core::chemical::rna::RNA_ResidueType
• chi_number_pseudoepsilon() : core::chemical::rna::RNA_ResidueType
• chi_number_pseudogamma() : core::chemical::rna::RNA_ResidueType
• chi_number_pseudozeta() : core::chemical::rna::RNA_ResidueType
• chi_poly_lookup() : core::scoring::hbonds::HBondDatabase
• chi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• chi_rmsd() : core::scoring::motif::MotifHit
• chi_rotamers() : core::chemical::ResidueType , core::conformation::Residue
• chi_sd() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_south_anti() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_south_syn() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_torsions() : core::io::silent::RNA_SilentStruct
• chidev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chidevpen() : core::pack::dunbrack::RotamerLibraryScratchSpace
• child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• child_index() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• chimean() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chisamples_for_rotamer_and_chi() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• chisd() : core::pack::dunbrack::RotamerLibraryScratchSpace
• ChiSet() : core::pack::dunbrack::ChiSet
• choose_effective_sequence_separation() : core::scoring::constraints::Constraint , core::scoring::constraints::MultiConstraint
• Ci() : core::scoring::FACTSResidueInfo
• ci_1b_types() : core::scoring::ScoreFunction
• ci_2b_begin() : core::scoring::ScoreFunction
• ci_2b_end() : core::scoring::ScoreFunction
• ci_2b_intrares_begin() : core::scoring::ScoreFunction
• ci_2b_intrares_end() : core::scoring::ScoreFunction
• ci_2b_types() : core::scoring::ScoreFunction
• ci_lr_2b_methods_begin() : core::scoring::ScoreFunction
• ci_lr_2b_methods_end() : core::scoring::ScoreFunction
• ci_lr_2b_types() : core::scoring::ScoreFunction
• ciBR() : core::pack::annealer::FASTERAnnealer
• Circle() : core::scoring::packstat::Circle
• CircularGeneral1D_Func() : core::scoring::func::CircularGeneral1D_Func
• CircularHarmonicFunc() : core::scoring::func::CircularHarmonicFunc
• CircularPowerFunc() : core::scoring::func::CircularPowerFunc
• CircularSigmoidalFunc() : core::scoring::func::CircularSigmoidalFunc
• cis_omega() : core::util::ABEGO
• clash_check() : core::scoring::motif::ResPairMotifQuery
• ClashBasedRepackShellSelector() : core::pack::task::residue_selector::ClashBasedRepackShellSelector
• class_name() : core::pack::task::residue_selector::AndResidueSelector , core::pack::task::residue_selector::ChainSelector , core::pack::task::residue_selector::ClashBasedRepackShellSelector , core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector , core::pack::task::residue_selector::JumpDownstreamSelector , core::pack::task::residue_selector::JumpUpstreamSelector , core::pack::task::residue_selector::NeighborhoodResidueSelector , core::pack::task::residue_selector::NotResidueSelector , core::pack::task::residue_selector::NumNeighborsSelector , core::pack::task::residue_selector::OrResidueSelector , core::pack::task::residue_selector::ResidueIndexSelector
• classification() : core::io::pdb::HeaderInformation
• classify_onebody_enmeth() : core::scoring::MinimizationNode
• classify_twobody_enmeth() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• clean_frag_cache() : core::fragment::FragmentIO
• clean_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• clean_up_rna_two_body_energy_tables() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• clear() : core::chemical::ResidueSelector , core::conformation::Conformation , core::fragment::Frame , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , core::graph::ArrayPool< T > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::id::SequenceMapping , core::io::sequence_comparation::DesignContrast , core::io::silent::SilentFileData , core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::MoveMap , core::kinematics::ResidueCoordinateChangeList , core::pack::annealer::SimAnnealerBase , core::pack::rotamer_set::WaterPackingInfo , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::PreventRepacking , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::TaskFactory , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver , core::pose::metrics::PoseMetricContainer , core::pose::PDBPoseMap , core::pose::Pose , core::scoring::CenHBPotential , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::ResidueConstraints , core::scoring::EMapVector , core::scoring::Energies , core::scoring::Hairpins , core::scoring::hbonds::HBondSet , core::scoring::motif::XformScore , core::scoring::NeighborList , core::scoring::SmoothScoreTermCoeffs , core::scoring::Strands , core::scoring::TMscoreStore , core::sequence::DP_Matrix , core::sequence::SequenceAlignment
• clear_() : core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl
• clear_active_dofs() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• clear_atoms() : core::optimization::DOF_Node
• clear_calculators() : core::pose::metrics::CalculatorFactory
• clear_comments() : core::io::silent::SilentStruct
• clear_compounds() : core::io::pdb::HeaderInformation
• clear_dCCdx_res_cache() : core::scoring::electron_density::ElectronDensity
• clear_dof_nodes() : core::optimization::MinimizerMap
• clear_energies() : core::io::silent::SilentStruct , core::scoring::Energies
• clear_events() : core::pose::datacache::LengthEventCollector
• clear_experimental_techniques() : core::io::pdb::HeaderInformation
• clear_extent_eval() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• clear_extent_gen() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• clear_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• clear_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• clear_hbonds() : core::scoring::hbonds::HBondResPairMinData
• clear_keywords() : core::io::pdb::HeaderInformation
• clear_observers() : core::conformation::Conformation
• clear_other_pose_list() : core::pose::full_model_info::FullModelInfo
• clear_parameters_list() : core::conformation::parametric::ParametersSet
• clear_parameters_set_list() : core::conformation::Conformation
• clear_properties() : core::chemical::AtomType
• clear_res_list() : core::pose::full_model_info::FullModelInfo
• clear_residue_connections() : core::conformation::Residue
• clear_residue_maps() : core::chemical::ResidueTypeSet
• clear_reslabel() : core::pose::PDBInfo
• clear_shared_silent_data() : core::io::silent::SilentFileData
• clear_structure_map() : core::io::raw_data::RawFileData , core::io::silent::SilentFileData
• clear_title() : core::io::pdb::HeaderInformation
• clear_two_body_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• clear_two_body_energy_for_edge() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• clear_Vall() : core::fragment::picking_old::FragmentLibraryManager
• clearMask() : core::scoring::electron_density::ElectronDensity
• clip_to_nrchi_range() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• Clone() : core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData
• clone() : core::chemical::ResidueType , core::conformation::Conformation , core::conformation::parametric::Parameters , core::conformation::parametric::ParametersSet , core::conformation::Residue , core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetricConformation , core::conformation::symmetry::SymmetryInfo , core::fragment::AnnotatedFragData , core::fragment::BaseCacheUnit , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::ConstantLengthFragSet , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::Frame , core::fragment::IndependentBBTorsionSRFD , core::fragment::JumpingFrame , core::fragment::MapCacheUnit< T > , core::fragment::NonContinuousFrame , core::fragment::OrderedFragSet , core::fragment::picking_old::concepts::ExtentEvaluator< Bookmark, Ext > , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::fragment::VectorCacheUnit< T > , core::grid::CartGrid< T > , core::id::CacheableAtomID_MapVector , 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 , core::kinematics::FoldTree , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::optimization::MinimizerOptions , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::DunbrackEnergy , core::pack::dunbrack::RotamerConstraint , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::pack::rotamer_set::AddResiduesRotamerSetOperation , core::pack::rotamer_set::RotamerSetOperation , core::pack::rotamer_set::UnboundRotamersOperation , core::pack::rotamer_set::WaterPackingInfo , core::pack::task::ALLAA , core::pack::task::ALLAAwc , core::pack::task::ALLAAxc , core::pack::task::APOLA , core::pack::task::APOLAR , core::pack::task::AUTO , core::pack::task::EMPTY , core::pack::task::EX , core::pack::task::EX_CUTOFF , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::NATAA , core::pack::task::NATRO , core::pack::task::NC , core::pack::task::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AllResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::NoResFilter , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilter , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoLacksLabel , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToInterface , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::TaskOperation , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::POLAR , core::pack::task::RESET , core::pack::task::ResfileCommand , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::TaskFactory , core::pack::task::USE_INPUT_SC , core::pose::datacache::CacheableObserver , core::pose::datacache::CacheablePoseRawPtr , core::pose::datacache::LengthEventCollector , core::pose::datacache::PositionConservedResiduesStore , core::pose::datacache::SpecialSegmentsObserver , core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::pose::Pose , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::CenListInfo , core::scoring::ChemicalShiftAnisotropy , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::CstEnergyContainer , core::scoring::constraints::CstMinimizationData , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::ContextGraph , core::scoring::cryst::XtalMLEnergy , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::custom_pair_distance::RespairInteractions , core::scoring::DenseEnergyContainer , core::scoring::DipolarCoupling , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfMinData , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::dna::BasePartner , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::DockingScoreFunction , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::FAElecContextData , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::Energies , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::CoarseEtableEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::TableLookupEtableEnergy , core::scoring::FACTSPoseInfo , core::scoring::FACTSResidueInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularGeneral1D_Func , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::scoring::GenBornPoseInfo , core::scoring::GenBornResidueInfo , core::scoring::GenBornRotamerSetInfo , 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::HBondResidueMinData , core::scoring::hbonds::HBondResPairMinData , core::scoring::hbonds::HBondSet , core::scoring::interface_::DDPscore , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::LREnergyContainer , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPLipoEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , core::scoring::methods::BurialEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CSD_TorsionEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::D2H_SA_Energy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::LK_SigmoidalFunc , core::scoring::methods::LKB_ResidueInfo , core::scoring::methods::LKB_ResiduesInfo , core::scoring::methods::LKB_ResPairMinData , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MetalloPlacementEnergy , core::scoring::methods::MissingEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OtherPoseEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PBLifetimeCache , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::RG_Energy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , core::scoring::methods::RG_MinData , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::MinScoreScoreFunction , core::scoring::NeighborList , core::scoring::nv::NVscore , core::scoring::OneToAllEnergyContainer , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::PeptideBondedEnergyContainer , core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::data::RNA_DataInfo , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::rna::RNA_ScoringInfo , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::ScoreFunction , core::scoring::SigmoidWeightedCenList< T > , core::scoring::solid_surface::SurfaceEnergies , core::scoring::SS_Info , core::scoring::SS_Killhairpins_Info , core::scoring::sym_e::symEnergy , core::scoring::symmetry::NBListCache , core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborGraph , core::scoring::trie::TrieCollection , core::scoring::TwelveANeighborGraph , core::scoring::vdwaals::VDW_Energy , core::sequence::CacheableSequenceProfile , core::sequence::ChemicalShiftScoringScheme , core::sequence::ChemicalShiftSequence , core::sequence::CompassScoringScheme , core::sequence::CompositeScoringScheme , core::sequence::CompositeSequence , core::sequence::DPScoringScheme , core::sequence::L1ScoringScheme , core::sequence::MatrixScoringScheme , core::sequence::PairScoringScheme , core::sequence::ProfSimScoringScheme , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceProfile , core::sequence::SimpleScoringScheme
• clone_as_base_class() : core::scoring::ScoreFunction
• clone_atom_types_from_commandline() : core::chemical::AtomTypeSet
• clone_cache_data() : core::fragment::Frame
• clone_calculators() : core::pose::metrics::PoseMetricContainer
• clone_info() : core::pose::full_model_info::FullModelInfo
• clone_shifted() : core::fragment::FragSet
• clone_with_frags() : core::fragment::Frame
• clone_with_new_sequence_numbering() : core::conformation::PseudoBondCollection
• clone_with_template() : core::fragment::Frame
• CloserToAtom() : core::scoring::sc::CloserToAtom
• cmp() : core::scoring::packstat::Event
• coarse_nchi() : core::coarse::Translator
• CoarseEtable() : core::coarse::CoarseEtable
• CoarseEtableEnergy() : core::scoring::etable::CoarseEtableEnergy
• CoarseRotamer() : core::pack::dunbrack::CoarseRotamer
• CoarseRotamerSet() : core::pack::dunbrack::CoarseRotamerSet
• CoarseSingleResidueLibrary() : core::pack::dunbrack::CoarseSingleResidueLibrary
• coarsify() : core::coarse::Translator , core::coarse::TranslatorSet , core::pack::dunbrack::CoarseSingleResidueLibrary
• code_to_root_map() : core::chemical::carbohydrates::CarbohydrateInfo
• collect_jumps() : core::environment::FoldTreeSketch::Node
• color_connected() : core::scoring::methods::IntermolEnergy
• cols() : core::sequence::DP_Matrix
• command_string() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• commands_for_residue() : core::pack::task::ResfileContents
• comment() : core::sequence::SequenceAlignment
• comment_from_line() : core::io::silent::SilentStruct
• comment_line() : core::io::silent::SilentFileData
• comment_lines() : core::io::silent::SilentFileData
• comments() : core::io::rna::RDAT , core::sequence::SequenceAlignment
• commit_change() : core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode
• commit_change_no_res_pointer_update() : core::pack::interaction_graph::SimpleNode
• commit_considered_substitution() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode
• commit_considered_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• CompassScoringScheme() : core::sequence::CompassScoringScheme
• complete_partial_state_assignment() : core::pack::interaction_graph::FASTERNode
• complete_state_assignment() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• components_moved_by_jump() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• compose_atoms() : core::chemical::sdf::MolWriter
• compose_bonds() : core::chemical::sdf::MolWriter
• compose_ctab() : core::chemical::sdf::MolWriter
• compose_job_info() : core::chemical::sdf::MolWriter
• compose_metadata() : core::chemical::sdf::MolWriter
• compose_naming() : core::chemical::sdf::MolWriter
• compose_nbr_atom() : core::chemical::sdf::MolWriter
• compose_properties() : core::chemical::sdf::MolWriter
• compose_rosetta_properties() : core::chemical::sdf::MolWriter
• compose_typeinfo() : core::chemical::sdf::MolWriter
• CompositeScoringScheme() : core::sequence::CompositeScoringScheme
• CompositeSequence() : core::sequence::CompositeSequence
• CompositeSequenceCreator() : core::sequence::CompositeSequenceCreator
• compound_in_progress() : core::io::pdb::HeaderInformation
• compound_token_to_string() : core::io::pdb::HeaderInformation
• compounds() : core::io::pdb::HeaderInformation
• compprob() : core::scoring::packstat::PackingScore
• compute() : core::scoring::dna::TorsionFourierComponent , core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairingSet , core::scoring::packstat::LeeRichards , core::scoring::packstat::Slice
• compute_centroid_environment() : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• compute_chi() : core::scoring::saxs::SAXSEnergy
• compute_chi_with_fit() : core::scoring::saxs::SAXSEnergy
• compute_csascore() : core::scoring::ChemicalShiftAnisotropy
• compute_dcentroid_environment() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• compute_dcscore() : core::scoring::DipolarCoupling
• compute_derivatives() : core::scoring::packstat::Slice
• compute_dipscore() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nls() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsDa() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsDaR() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsR() : core::scoring::ResidualDipolarCoupling
• compute_dist_map() : core::kinematics::ShortestPathInFoldTree
• compute_distance_histogram() : core::scoring::saxs::SAXSEnergy
• compute_energies() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• compute_energy() : core::pack::interaction_graph::SimpleEdge
• compute_events() : core::scoring::packstat::Slice
• compute_fa_deriv() : core::scoring::membrane::FaMPEnvEnergy
• compute_fa_proj() : core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy
• compute_fa_proj_coord() : core::scoring::membrane::FaMPEnvEnergy
• compute_fa_projection() : core::scoring::Membrane_FAPotential
• compute_fractions() : core::fragment::SecondaryStructure
• compute_func() : core::scoring::func::SoedingFunc
• compute_grid_constant() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_intensities() : core::scoring::saxs::SAXSEnergy
• compute_jumpout_diff() : core::scoring::geometric_solvation::DatabaseOccSolEne
• compute_L1() : core::scoring::saxs::SAXSEnergy
• compute_matching_energy() : core::scoring::disulfides::DisulfideMatchingPotential
• compute_max_branch_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• compute_membrane_embedding() : core::scoring::MembranePotential
• compute_metrics() : core::scoring::motif::MotifHits
• compute_mpair_score() : core::scoring::membrane::MPPairEnergy
• compute_mpcbeta_score() : core::scoring::membrane::MPCbetaEnergy
• compute_mpenv_score() : core::scoring::membrane::MPEnvEnergy
• compute_nonhelix_penalty() : core::scoring::membrane::MPNonHelixPenalty
• compute_normalization() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• compute_one_and_two_body_energies() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• compute_one_body_energies() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• compute_one_body_energy_maps() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• compute_orb_orb_E() : core::scoring::orbitals::OrbitalsScore
• compute_pair_energy_for_alternate_state() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• compute_pair_energy_for_current_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• compute_polar_group_sol_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_pose_hpatch_score() : core::pack::interaction_graph::SurfacePotential
• compute_pose_surface_energy() : core::pack::interaction_graph::SurfacePotential
• compute_proline_correction_energies_for_otf_graph() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• compute_residue_surface_energy() : core::pack::interaction_graph::SurfacePotential
• compute_rho() : core::scoring::electron_density::ElectronDensity
• compute_rotamer_pair_energy() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• compute_smooth_nb() : core::scoring::packing::PoseBalls
• compute_surface() : core::scoring::packstat::Slice
• compute_surrounding_sasa() : core::scoring::packstat::MultiProbePerSphereAccumulator
• compute_symm_rotations() : core::scoring::electron_density::ElectronDensity
• compute_tensor_stats() : core::scoring::ResidualDipolarCoupling
• compute_termini_penalty() : core::scoring::membrane::MPTerminiPenalty
• compute_tmproj_penalty() : core::scoring::membrane::MPTMProjPenalty
• compute_zero_intensity() : core::scoring::saxs::SAXSEnergy
• computeCrystParams() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• computeGradients() : core::scoring::electron_density::ElectronDensity
• computeStats() : core::scoring::electron_density::ElectronDensity
• concatenate_topology() : core::conformation::membrane::SpanningTopology
• conditional_erase() : core::pose::PDBPoseMap
• conditionally_add_edge() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• confidence() : core::fragment::SecondaryStructure
• Conformation() : core::conformation::Conformation
• conformation() : core::pose::Pose
• conformation_energy() : core::scoring::constraints::Constraints
• conformation_ptr() : core::pose::Pose
• ConformationEvent() : core::pose::signals::ConformationEvent
• ConformationXYZ() : core::scoring::func::ConformationXYZ
• conformers_for_ring_size() : core::chemical::RingConformerSet
• conjugability() : core::chemical::Bond
• conn_dat() : core::scoring::etable::etrie::CountPairDataGeneric
• conn_dist() : core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric
• connect_atom() : core::conformation::Residue
• connect_map() : core::conformation::Residue
• connect_map_size() : core::conformation::Residue
• connected() : core::kinematics::FoldTree
• connected_by_twobonds() : core::scoring::methods::GoapRsdType
• connected_residue_at_resconn() : core::conformation::Residue
• connection_distance() : core::conformation::Residue
• connection_exists_to_residue() : core::scoring::trie::RotamerTrieBase
• connection_id_for_residue() : core::scoring::trie::RotamerTrieBase
• connection_incomplete() : core::conformation::Residue
• connection_index() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_pair() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_use_theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• ConnectionEvent() : core::conformation::signals::ConnectionEvent
• connections_match() : core::conformation::Residue
• connections_to_residue() : core::conformation::Residue
• connid() : core::chemical::ResConnID
• connid_for_entry_connpoint() : core::scoring::trie::CPDataCorrespondence
• consider_alternate_state() : core::pack::interaction_graph::HPatchNode< V, E, G >
• consider_substitution() : 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::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• considering_alternate_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• const_begin() : core::graph::EdgeList
• const_edge() : core::graph::EdgeListElement
• const_edge_list_begin() : core::graph::Graph , core::graph::Node
• const_edge_list_end() : core::graph::Graph , core::graph::Node
• const_end() : core::graph::EdgeList
• const_iterator() : core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::const_iterator
• const_last() : core::graph::EdgeList
• const_lower_edge_list_begin() : core::graph::Node
• const_lower_edge_list_end() : core::graph::Node
• const_neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• const_neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• const_next() : core::graph::EdgeListElement
• const_previous() : core::graph::EdgeListElement
• const_residues() : core::conformation::Conformation
• const_upper_edge_list_begin() : core::graph::Node , core::graph::UEVertex< V, E >
• const_upper_edge_list_end() : core::graph::Node , core::graph::UEVertex< V, E >
• const_upper_neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• const_upper_neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• ConstantConstraint() : core::scoring::constraints::ConstantConstraint
• ConstantFunc() : core::scoring::func::ConstantFunc
• ConstantLengthFragSet() : core::fragment::ConstantLengthFragSet
• ConstantLengthFragSetIterator_() : core::fragment::ConstantLengthFragSetIterator_
• ConstFrameIterator() : core::fragment::ConstFrameIterator
• Constraint() : core::scoring::constraints::Constraint
• constraint_set() : core::pose::Pose
• ConstraintCreator() : core::scoring::constraints::ConstraintCreator
• ConstraintEdge() : core::scoring::constraints::ConstraintEdge
• ConstraintFactory() : core::scoring::constraints::ConstraintFactory
• ConstraintGraph() : core::scoring::constraints::ConstraintGraph
• ConstraintIO() : core::scoring::constraints::ConstraintIO
• ConstraintNode() : core::scoring::constraints::ConstraintNode
• ConstraintRegistrator() : core::scoring::constraints::ConstraintRegistrator< T >
• Constraints() : core::scoring::constraints::Constraints
• constraints() : core::scoring::constraints::Constraints , core::scoring::constraints::CstMinimizationData
• ConstraintsEnergy() : core::scoring::constraints::ConstraintsEnergy
• ConstraintSet() : core::scoring::constraints::ConstraintSet
• construct_rotamer_trie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• contact_order() : core::scoring::dssp::StrandPairing
• ContactOrderEnergy() : core::scoring::methods::ContactOrderEnergy
• contains() : core::scoring::dssp::StrandPairing , core::scoring::packstat::Circle , core::scoring::packstat::Octree2D
• contains_atom_type() : core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet
• contains_bond_length() : core::chemical::IdealBondLengthSet
• contains_carbohydrate_residues() : core::conformation::Conformation
• contains_element_type() : core::chemical::ElementSet
• contains_seqpos() : core::fragment::Frame
• context_derivative_empty() : core::scoring::FACTSPoseInfo
• context_graph() : core::scoring::Energies
• context_graphs() : core::scoring::Energies
• ContextDependentGeometricSolEnergy() : core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy
• ContextDependentLRTwoBodyEnergy() : core::scoring::methods::ContextDependentLRTwoBodyEnergy
• ContextDependentOneBodyEnergy() : core::scoring::methods::ContextDependentOneBodyEnergy
• ContextDependentTwoBodyEnergy() : core::scoring::methods::ContextDependentTwoBodyEnergy
• ContextGraph() : core::scoring::ContextGraph
• ContextIndependentGeometricSolEnergy() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
• ContextIndependentLRTwoBodyEnergy() : core::scoring::methods::ContextIndependentLRTwoBodyEnergy
• ContextIndependentOneBodyEnergy() : core::scoring::methods::ContextIndependentOneBodyEnergy
• ContextIndependentTwoBodyEnergy() : core::scoring::methods::ContextIndependentTwoBodyEnergy
• contiguous_monomers() : core::conformation::symmetry::SymmetryInfo
• continuous() : core::scoring::methods::GoapEnergy
• ContinuousRotamerSet() : core::pack::rotamer_set::ContinuousRotamerSet
• ContinuousRotamerSets() : core::pack::rotamer_set::ContinuousRotamerSets
• conventional_chains() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• conventional_numbering() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• conventional_to_full() : core::pose::full_model_info::FullModelParameters
• convert_FArray2D_to_vector0() : core::scoring::TMscore
• convert_profile_to_probs() : core::sequence::SequenceProfile
• convert_to_parameter_values_at_res() : core::pose::full_model_info::FullModelParameters
• convert_to_res_lists_by_value() : core::pose::full_model_info::FullModelParameters
• convert_to_ResidueType() : core::chemical::sdf::MolFileIOMolecule
• cool() : core::pack::annealer::MultiCoolAnnealer
• coord() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• coordinate_constraint_energy() : core::scoring::constraints::ConstraintEdge
• CoordinateConstraint() : core::scoring::constraints::CoordinateConstraint
• CoordinateConstraintCreator() : core::scoring::constraints::CoordinateConstraintCreator
• coordinates_per_fragment() : core::indexed_structure_store::FragmentSpecification
• Coordinates_Tetrahedral_bondedto3atoms_helper() : core::chemical::orbitals::AssignOrbitals
• Coordinates_TriganolPlanar_bondedto1atom_helper() : core::chemical::orbitals::AssignOrbitals
• CoordinatesDihedral() : core::scoring::orbitals::OrbitalsAssigned
• CoordinatesTetrahedral() : core::scoring::orbitals::OrbitalsAssigned
• coords() : core::grid::CartGrid< T > , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pose::MiniPose , core::pose::UnrecognizedAtomRecord
• coords_vector() : core::conformation::UltraLightResidue
• copy() : core::fragment::AnnotatedFragData , core::fragment::FragData , core::pack::interaction_graph::RotamerDots , core::pose::PDBInfo
• copy_array_contents() : core::graph::ArrayPoolElement< T >
• copy_bb_donor_acceptor_arrays() : core::scoring::hbonds::HBondSet
• copy_connectivity() : core::graph::Graph
• copy_context_graphs() : core::scoring::Energies
• copy_coords() : core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pack::scmin::ResidueAtomTreeCollectionMomento
• copy_data() : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueProperties , core::chemical::RingConformerSet , core::conformation::membrane::LipidAccInfo
• copy_dofs_from_pose() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• copy_dofs_info() : core::pose::copydofs::CopyDofs
• copy_dofs_to_pose() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• copy_from() : core::graph::Edge , core::graph::Node , core::graph::UpperEdgeGraph< V, E > , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleNode , core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintNode , core::scoring::constraints::Constraints , core::scoring::EnergyEdge , core::scoring::EnergyNode , core::scoring::etable::MembEtable , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborNode
• copy_length_events() : core::pose::datacache::LengthEventCollector
• copy_lr_energy_containers() : core::scoring::Energies
• copy_nblists() : core::scoring::Energies
• copy_old_data_into_new_table() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• copy_operations() : core::pack::task::TaskFactory
• copy_opts_swapped() : core::scoring::motif::ResPairMotifQuery
• copy_residue_connections() : core::conformation::Residue
• copy_residue_connections_from() : core::conformation::Residue
• copy_scores() : core::io::silent::SilentStruct
• copy_segment() : core::conformation::Conformation , core::pose::Pose
• copy_values() : core::scoring::rna::RNA_RawBaseBaseInfo
• CopyDofs() : core::pose::copydofs::CopyDofs
• CopyEdge() : core::chemical::CopyEdge< Graph1, Graph2 >
• CopyVertex() : core::chemical::CopyVertex< Graph1, Graph2 >
• COradius2() : core::scoring::FACTSRsdTypeInfo
• correct_arrays_for_symmetry() : core::scoring::symmetry::SymmetricScoreFunction
• correct_finalize_score() : core::scoring::symmetry::SymmetricScoreFunction
• correct_termini_derivatives() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
• cosAHD_fade_lookup() : core::scoring::hbonds::HBondDatabase
• cosAHD_long_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosAHD_short_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_fade_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_long_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_short_poly_lookup() : core::scoring::hbonds::HBondDatabase
• CouldHaveHybridization() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• coulomb() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::GroupElec
• Coulomb() : core::scoring::etable::coulomb::Coulomb
• coulomb() : core::scoring::rna::StackElecEnergy
• count() : core::import_pose::atom_tree_diffs::AtomTreeDiff , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , core::scoring::etable::count_pair::CountPairNone , core::scoring::motif::ResPairMotif , core::sequence::CompositeScoringScheme
• count_at_path_distance() : core::scoring::etable::count_pair::CountPairCrossover3 , core::scoring::etable::count_pair::CountPairCrossover4
• count_atoms() : core::scoring::APBSWrapper
• count_atoms_in_common() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• count_connected_components_and_initialize_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• count_dynamic_memory() : core::graph::Edge , core::graph::Graph , core::graph::Node , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::FirstClassEdge< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyNode , core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::ConstraintNode , core::scoring::ContextGraph , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::EnergyNode , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::scoring::MinimizationNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::scoring::TwelveANeighborNode
• count_ff() : core::scoring::saxs::FormFactorManager
• count_fixed_residues() : core::kinematics::FoldTree
• count_motifs() : core::scoring::motif::MotifHash
• count_num_covered() : core::pack::interaction_graph::DotSphere
• count_scoring_atoms() : core::scoring::saxs::SAXSEnergy
• count_static_memory() : core::graph::Edge , core::graph::Graph , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyNode , core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::ConstraintNode , core::scoring::ContextGraph , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::EnergyNode , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::scoring::MinimizationNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::scoring::TwelveANeighborNode
• count_water() : core::pack::task::residue_selector::NumNeighborsSelector
• CountPair1B() : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
• CountPairAll() : core::scoring::etable::count_pair::CountPairAll
• CountPairData_1_1() : core::scoring::etable::etrie::CountPairData_1_1
• CountPairDataGeneric() : core::scoring::etable::etrie::CountPairDataGeneric
• CountPairFunction() : core::scoring::etable::count_pair::CountPairFunction
• CountPairGeneric() : core::scoring::etable::count_pair::CountPairGeneric
• CountPairIntraRes() : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >
• CountPairIntraResC3() : core::scoring::etable::count_pair::CountPairIntraResC3
• CountPairIntraResC4() : core::scoring::etable::count_pair::CountPairIntraResC4
• CountPairNone() : core::scoring::etable::count_pair::CountPairNone
• CountUnsaturatedNeighbors() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• CountViolFunc() : core::scoring::func::CountViolFunc
• cp_data() : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA >
• cp_function() : core::scoring::orbitals::OrbitalsAssigned
• CPDataCorrespondence() : core::scoring::trie::CPDataCorrespondence
• cprev_n_bond_length_params() : core::scoring::methods::ResidueCartBondedParameters
• crd() : core::scoring::methods::ProQ_Energy
• create() : core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::IndependentBBTorsionSRFD , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver
• create_adduct_combinations() : core::chemical::ResidueTypeSet
• create_annealer() : core::pack::annealer::AnnealerFactory
• create_atom_type_from_database() : core::chemical::AtomTypeSet
• create_atom_type_set() : core::chemical::ChemicalManager
• create_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• create_background_node() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• create_centroid_rotamer_libraries_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_constraint() : core::pack::dunbrack::DunbrackConstraintCreator , core::scoring::constraints::AmbiguousConstraintCreator , core::scoring::constraints::AmbiguousNMRConstraintCreator , core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator , core::scoring::constraints::AngleConstraintCreator , core::scoring::constraints::AtomPairConstraintCreator , core::scoring::constraints::BigBinConstraintCreator , core::scoring::constraints::ConstraintCreator , core::scoring::constraints::CoordinateConstraintCreator , core::scoring::constraints::DihedralConstraintCreator , core::scoring::constraints::DihedralPairConstraintCreator , core::scoring::constraints::FabConstraintCreator , core::scoring::constraints::KofNConstraintCreator , core::scoring::constraints::LocalCoordinateConstraintCreator , core::scoring::constraints::MultiConstraintCreator , core::scoring::constraints::SequenceProfileConstraintCreator , core::scoring::constraints::SiteConstraintCreator , core::scoring::constraints::SiteConstraintResiduesCreator
• create_context_graph() : core::scoring::ContextGraphFactory
• create_count_pair_function() : core::scoring::etable::count_pair::CountPairFactory
• create_count_pair_function_and_invoke() : core::scoring::etable::count_pair::CountPairFactory
• create_element_set() : core::chemical::ChemicalManager
• create_energy_method() : core::pack::dunbrack::cenrot::CenRotDunEnergyCreator , core::pack::dunbrack::DunbrackEnergyCreator , core::pack::interaction_graph::HPatchEnergyCreator , core::pack::interaction_graph::SurfaceEnergyCreator , core::scoring::carbon_hbonds::CarbonHBondEnergyCreator , core::scoring::constraints::ConstraintsEnergyCreator , core::scoring::cryst::XtalMLEnergyCreator , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator , core::scoring::disulfides::CentroidDisulfideEnergyCreator , core::scoring::disulfides::DisulfideMatchingEnergyCreator , core::scoring::disulfides::FullatomDisulfideEnergyCreator , core::scoring::dna::DNAChiEnergyCreator , core::scoring::dna::DNATorsionEnergyCreator , core::scoring::elec::FA_ElecEnergyAroAllCreator , core::scoring::elec::FA_ElecEnergyAroAroCreator , core::scoring::elec::FA_ElecEnergyCreator , core::scoring::elec::FA_GrpElecEnergyCreator , core::scoring::elec::RNA_FA_ElecEnergyCreator , core::scoring::electron_density::ElecDensAllAtomCenEnergyCreator , core::scoring::electron_density::ElecDensCenEnergyCreator , core::scoring::electron_density::ElecDensEnergyCreator , core::scoring::electron_density::FastDensEnergyCreator , core::scoring::electron_density::PattersonCorrEnergyCreator , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator , core::scoring::etable::CoarseEtableEnergyCreator , core::scoring::etable::EtableClassicIntraEnergyCreator , core::scoring::etable::EtableEnergyCreator , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergyCreator , core::scoring::hackaro::HackAroEnergyCreator , core::scoring::hbonds::HBondEnergyCreator , core::scoring::interface_::DDPscoreCreator , core::scoring::loop_graph::LoopCloseEnergyCreator , core::scoring::membrane::FaMPEnvEnergyCreator , core::scoring::membrane::FaMPEnvSmoothEnergyCreator , core::scoring::membrane::FaMPSolvEnergyCreator , core::scoring::membrane::MPCbetaEnergyCreator , core::scoring::membrane::MPEnvEnergyCreator , core::scoring::membrane::MPLipoEnergyCreator , core::scoring::membrane::MPNonHelixPenaltyCreator , core::scoring::membrane::MPPairEnergyCreator , core::scoring::membrane::MPTerminiPenaltyCreator , core::scoring::membrane::MPTMProjPenaltyCreator , core::scoring::methods::BurialEnergyCreator , core::scoring::methods::CartesianBondedEnergyCreator , core::scoring::methods::CenHBEnergyCreator , core::scoring::methods::CenPairEnergyCreator , core::scoring::methods::CenRotEnvEnergyCreator , core::scoring::methods::CenRotPairEnergyCreator , core::scoring::methods::ChainbreakEnergyCreator , core::scoring::methods::ChemicalShiftAnisotropyEnergyCreator , core::scoring::methods::ContactOrderEnergyCreator , core::scoring::methods::CustomAtomPairEnergyCreator , core::scoring::methods::D2H_SA_EnergyCreator , core::scoring::methods::dfire::DFIRE_EnergyCreator , core::scoring::methods::DipolarCouplingEnergyCreator , core::scoring::methods::DirectReadoutEnergyCreator , core::scoring::methods::DistanceChainbreakEnergyCreator , core::scoring::methods::DNA_BaseEnergyCreator , core::scoring::methods::EnergyMethodCreator , core::scoring::methods::EnvEnergyCreator , core::scoring::methods::EnvSmoothEnergyCreator , core::scoring::methods::Fa_MbenvEnergyCreator , core::scoring::methods::Fa_MbsolvEnergyCreator , core::scoring::methods::FACTSEnergyCreator , core::scoring::methods::FreeDOF_EnergyCreator , core::scoring::methods::GaussianOverlapEnergyCreator , core::scoring::methods::GenBornEnergyCreator , core::scoring::methods::GoapEnergyCreator , core::scoring::methods::HybridVDW_EnergyCreator , core::scoring::methods::IntermolEnergyCreator , core::scoring::methods::LinearChainbreakEnergyCreator , core::scoring::methods::LK_BallEnergyCreator , core::scoring::methods::LK_hackCreator , core::scoring::methods::LK_PolarNonPolarEnergyCreator , core::scoring::methods::MembraneCbetaEnergyCreator , core::scoring::methods::MembraneCenPairEnergyCreator , core::scoring::methods::MembraneEnvEnergyCreator , core::scoring::methods::MembraneEnvPenaltiesCreator , core::scoring::methods::MembraneEnvSmoothEnergyCreator , core::scoring::methods::MembraneLipoCreator , core::scoring::methods::MissingEnergyCreator , core::scoring::methods::MMBondAngleEnergyCreator , core::scoring::methods::MMBondLengthEnergyCreator , core::scoring::methods::MMLJEnergyInterCreator , core::scoring::methods::MMLJEnergyIntraCreator , core::scoring::methods::MMTorsionEnergyCreator , core::scoring::methods::NMerPSSMEnergyCreator , core::scoring::methods::NMerRefEnergyCreator , core::scoring::methods::NMerSVMEnergyCreator , core::scoring::methods::OmegaTetherEnergyCreator , core::scoring::methods::OtherPoseEnergyCreator , core::scoring::methods::P_AA_EnergyCreator , core::scoring::methods::P_AA_pp_EnergyCreator , core::scoring::methods::PackStatEnergyCreator , core::scoring::methods::PairEnergyCreator , core::scoring::methods::PeptideBondEnergyCreator , core::scoring::methods::pHEnergyCreator , core::scoring::methods::PoissonBoltzmannEnergyCreator , core::scoring::methods::ProClosureEnergyCreator , core::scoring::methods::ProQ_EnergyCreator , core::scoring::methods::Rama2BOffsetEnergyCreator , core::scoring::methods::RamachandranEnergy2BCreator , core::scoring::methods::RamachandranEnergyCreator , core::scoring::methods::ReferenceEnergyCreator , core::scoring::methods::ReferenceEnergyNoncanonicalCreator , core::scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator , core::scoring::methods::ResidualDipolarCouplingEnergyCreator , core::scoring::methods::RG_Energy_FastCreator , core::scoring::methods::RG_LocalEnergyCreator , core::scoring::methods::RMS_EnergyCreator , core::scoring::methods::SA_EnergyCreator , core::scoring::methods::SecondaryStructureEnergyCreator , core::scoring::methods::SequenceDependentRefEnergyCreator , core::scoring::methods::SmoothCenPairEnergyCreator , core::scoring::methods::SmoothEnvEnergyCreator , core::scoring::methods::SuckerEnergyCreator , core::scoring::methods::SymmetricLigandEnergyCreator , core::scoring::methods::UnfoldedStateEnergyCreator , core::scoring::methods::WaterAdductHBondEnergyCreator , core::scoring::methods::WaterAdductIntraEnergyCreator , core::scoring::methods::YHHPlanarityEnergyCreator , core::scoring::nv::NVscoreCreator , core::scoring::orbitals::OrbitalsScoreCreator , core::scoring::packing::HolesEnergyCreator , core::scoring::packing::SurfEnergyCreator , core::scoring::packing::SurfVolEnergyCreator , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergyCreator , core::scoring::rna::data::RNA_ChemicalMappingEnergyCreator , core::scoring::rna::data::RNA_DataBackboneEnergyCreator , core::scoring::rna::RG_Energy_RNACreator , core::scoring::rna::RNA_BulgeEnergyCreator , core::scoring::rna::RNA_FullAtomStackingEnergyCreator , core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator , core::scoring::rna::RNA_JR_SuiteEnergyCreator , core::scoring::rna::RNA_LJ_BaseEnergyCreator , core::scoring::rna::RNA_Mg_EnergyCreator , core::scoring::rna::RNA_PairwiseLowResolutionEnergyCreator , core::scoring::rna::RNA_SugarCloseEnergyCreator , core::scoring::rna::RNA_SuiteEnergyCreator , core::scoring::rna::RNA_TorsionEnergyCreator , core::scoring::rna::RNA_VDW_EnergyCreator , core::scoring::rna::StackElecEnergyCreator , core::scoring::saxs::FastSAXSEnergyCreator , core::scoring::saxs::SAXSEnergy , core::scoring::saxs::SAXSEnergyCreator , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::sym_e::symECreator , core::scoring::vdwaals::VDW_EnergyCreator
• create_fa_dunbrack_libraries() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_02_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_02_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_10_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_10_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_from_spanfile() : core::conformation::membrane::SpanningTopology
• create_from_structure() : core::conformation::membrane::SpanningTopology
• create_ideal_bond_length_set() : core::chemical::ChemicalManager
• create_info() : core::scoring::FACTSRsdTypeInfo
• create_interaction_graph() : core::pack::interaction_graph::InteractionGraphFactory
• create_intrares_count_pair_function() : core::scoring::etable::count_pair::CountPairFactory
• create_mm_atom_type_set() : core::chemical::ChemicalManager
• create_new_block() : core::graph::ArrayPool< T >
• create_new_edge() : core::graph::Graph , 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::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::scoring::constraints::ConstraintGraph , core::scoring::EnergyGraph , core::scoring::MinimizationGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• create_new_node() : core::graph::Graph , 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::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::scoring::constraints::ConstraintGraph , core::scoring::EnergyGraph , core::scoring::MinimizationGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• create_new_parameters_set() : core::conformation::Conformation
• create_options() : core::chemical::ResidueLoaderOptionsCreator , core::conformation::symmetry::SymmDataOptionsCreator , core::import_pose::ImportPoseOptionsCreator , core::io::silent::SilentFileOptionsCreator , core::scoring::electron_density::ElectronDensityOptionsCreator
• create_orbital_type_set() : core::chemical::ChemicalManager
• create_packer_task() : core::pack::task::TaskFactory
• create_parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• create_res_filter() : core::pack::task::operation::AllResFilterCreator , core::pack::task::operation::AnyResFilterCreator , core::pack::task::operation::ChainIsCreator , core::pack::task::operation::ChainIsntCreator , core::pack::task::operation::NoResFilterCreator , core::pack::task::operation::ResFilterCreator , core::pack::task::operation::ResidueHasPropertyCreator , core::pack::task::operation::ResidueIndexIsCreator , core::pack::task::operation::ResidueIndexIsntCreator , core::pack::task::operation::ResidueLacksPropertyCreator , core::pack::task::operation::ResidueName3IsCreator , core::pack::task::operation::ResidueName3IsntCreator , core::pack::task::operation::ResiduePDBIndexIsCreator , core::pack::task::operation::ResiduePDBIndexIsntCreator , core::pack::task::operation::ResiduePDBInfoHasLabelCreator , core::pack::task::operation::ResiduePDBInfoLacksLabelCreator , core::pack::task::operation::ResidueTypeFilterCreator
• create_res_level_task_operation() : core::pack::task::operation::AddBehaviorRLTCreator , core::pack::task::operation::DisallowIfNonnativeRLTCreator , core::pack::task::operation::PreventRepackingRLTCreator , core::pack::task::operation::ResLvlTaskOperationCreator , core::pack::task::operation::RestrictAbsentCanonicalAASRLTCreator , core::pack::task::operation::RestrictToRepackingRLTCreator
• create_residue() : core::conformation::Residue , core::conformation::ResidueFactory
• create_residue_selector() : core::pack::task::residue_selector::AndResidueSelectorCreator , core::pack::task::residue_selector::ChainSelectorCreator , core::pack::task::residue_selector::ClashBasedRepackShellSelectorCreator , core::pack::task::residue_selector::InterGroupInterfaceByVectorSelectorCreator , core::pack::task::residue_selector::JumpDownstreamSelectorCreator , core::pack::task::residue_selector::JumpUpstreamSelectorCreator , core::pack::task::residue_selector::NeighborhoodResidueSelectorCreator , core::pack::task::residue_selector::NotResidueSelectorCreator , core::pack::task::residue_selector::NumNeighborsSelectorCreator , core::pack::task::residue_selector::OrResidueSelectorCreator , core::pack::task::residue_selector::ResidueIndexSelectorCreator , core::pack::task::residue_selector::ResidueSelectorCreator
• create_residue_type_set() : core::chemical::ChemicalManager
• create_resource() : core::chemical::ResidueLoader , core::conformation::symmetry::SymmDataLoader , core::import_pose::PoseFromPDBLoader , core::io::silent::SilentFileLoader , core::scoring::electron_density::ElectronDensityLoader
• create_resource_loader() : core::chemical::ResidueLoaderCreator , core::conformation::symmetry::SymmDataLoaderCreator , core::import_pose::PoseFromPDBLoaderCreator , core::io::silent::SilentFileLoaderCreator , core::scoring::electron_density::ElectronDensityLoaderCreator
• create_rotamer() : core::conformation::Residue
• create_rotamer_set() : core::pack::rotamer_set::RotamerSetFactory , core::pack::rotamer_set::symmetry::SymmetricRotamerSetFactory
• create_rotamer_trie() : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDW_Energy
• create_rotamer_trie_1() : core::scoring::etable::BaseEtableEnergy< Derived >
• create_rotamer_trie_2() : core::scoring::etable::BaseEtableEnergy< Derived >
• create_rotameric_dunlib() : core::pack::dunbrack::RotamerLibrary
• create_rotamers_from_chisets() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
• create_score_function() : core::scoring::ScoreFunctionFactory
• create_semi_rotameric_dunlib() : core::pack::dunbrack::RotamerLibrary
• create_sequence() : core::sequence::ChemicalShiftSequenceCreator , core::sequence::CompositeSequenceCreator , core::sequence::SequenceCouplingCreator , core::sequence::SequenceCreator , core::sequence::SequenceProfileCreator , core::sequence::SimpleSequenceCreator
• create_silent_struct() : core::import_pose::PDBSilentStructCreator , core::io::silent::BinarySilentStructCreator , core::io::silent::ProteinSilentStruct_SinglePrecCreator , core::io::silent::ProteinSilentStructCreator , core::io::silent::RigidBodySilentStructCreator , core::io::silent::RNA_SilentStructCreator , core::io::silent::ScoreFileSilentStructCreator , core::io::silent::ScoreJumpFileSilentStructCreator , core::io::silent::SilentStructCreator
• create_SilentStructOP() : core::io::silent::SilentFileData
• create_singleton_instance() : core::chemical::ChemicalManager , core::chemical::orbitals::OrbitalTypeMapper , core::fragment::picking_old::FragmentLibraryManager , core::indexed_structure_store::StructureStoreManager , core::io::silent::SilentStructFactory , core::pack::dunbrack::RotamerLibrary , core::pack::interaction_graph::RotamerDotsRadiusData , core::pack::interaction_graph::SurfacePotential , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::scoring::constraints::ConstraintFactory , core::scoring::constraints::ConstraintIO , core::scoring::geometric_solvation::GridInfo , core::scoring::geometric_solvation::WaterWeightGridSet , core::scoring::saxs::SinXOverX , core::scoring::ScoringManager , core::sequence::SequenceFactory
• create_srdl() : core::pack::dunbrack::RotamerLibrary
• create_symm_data() : core::conformation::symmetry::SymmDataFactory
• create_task_and_apply_taskoperations() : core::pack::task::TaskFactory
• create_task_operation() : core::pack::task::operation::AppendResidueRotamerSetCreator , core::pack::task::operation::AppendRotamerCreator , core::pack::task::operation::AppendRotamerSetCreator , core::pack::task::operation::DisallowIfNonnativeCreator , core::pack::task::operation::ExtraChiCutoffCreator , core::pack::task::operation::ExtraRotamersCreator , core::pack::task::operation::ExtraRotamersGenericCreator , core::pack::task::operation::IncludeCurrentCreator , core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator , core::pack::task::operation::InitializeFromCommandlineCreator , core::pack::task::operation::NoRepackDisulfidesCreator , core::pack::task::operation::OperateOnCertainResiduesCreator , core::pack::task::operation::OperateOnResidueSubsetCreator , core::pack::task::operation::OptCysHGCreator , core::pack::task::operation::OptHCreator , core::pack::task::operation::PreserveCBetaCreator , core::pack::task::operation::PreventRepackingCreator , core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator , core::pack::task::operation::ReadResfileCreator , core::pack::task::operation::ReplicateTaskCreator , core::pack::task::operation::RestrictAbsentCanonicalAASCreator , core::pack::task::operation::RestrictResidueToRepackingCreator , core::pack::task::operation::RestrictToRepackingCreator , core::pack::task::operation::RestrictYSDesignCreator , core::pack::task::operation::RotamerExplosionCreator , core::pack::task::operation::SetRotamerCouplingsCreator , core::pack::task::operation::SetRotamerLinksCreator , core::pack::task::operation::TaskOperationCreator
• create_vertices() : core::graph::UpperEdgeGraph< V, E >
• create_working_data() : core::io::pdb::FileData
• CreateAtomicEnvironmentToTypesMap() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• createFileData() : core::io::pdb::PDB_DReader
• createPDBData() : core::io::pdb::PDB_DReader
• createPDBData_vector() : core::io::pdb::PDB_DReader
• createPDBString() : core::io::pdb::PDB_DReader
• createRecords() : core::io::pdb::PDB_DReader
• cross_over() : core::optimization::GA_Minimizer
• cross_product_helper() : core::chemical::orbitals::AssignOrbitals
• crossover() : core::scoring::etable::etrie::TrieCountPairGeneric
• CrystInfo() : core::pose::CrystInfo
• crystinfo() : core::pose::PDBInfo
• CSA() : core::scoring::CSA
• csa_from_pose() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• CSAcomputed() : core::scoring::CSA
• CSAerr() : core::scoring::CSA
• CSAval() : core::scoring::CSA
• CSD_TorsionEnergy() : core::scoring::methods::CSD_TorsionEnergy
• cst_max_seq_sep() : core::scoring::methods::EnergyMethodOptions
• cst_set() : core::pose::full_model_info::FullModelParameters
• cst_string() : core::pose::full_model_info::FullModelParameters
• CstEnergyContainer() : core::scoring::constraints::CstEnergyContainer
• CstMinimizationData() : core::scoring::constraints::CstMinimizationData
• CstResNeighbConstIterator() : core::scoring::constraints::CstResNeighbConstIterator
• CstResNeighbIterator() : core::scoring::constraints::CstResNeighbIterator
• CtabParserBase() : core::chemical::sdf::CtabParserBase
• cubic_interpolation() : core::optimization::LineMinimizationAlgorithm
• cubic_polynomial_deriv() : core::scoring::etable::Etable
• cubic_polynomial_from_spline() : core::scoring::etable::Etable
• CubicPolynomial() : core::scoring::etable::CubicPolynomial
• curr_sc_centroid() : core::pack::interaction_graph::SimpleNode
• curr_sc_radius() : core::pack::interaction_graph::SimpleNode
• curr_state_energy() : core::pack::interaction_graph::SymmMinimalistEdge
• curr_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_inv_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G >
• current_binary_format_version_id_02() : core::pack::dunbrack::RotamerLibrary
• current_binary_format_version_id_10() : core::pack::dunbrack::RotamerLibrary
• current_distance() : core::scoring::loop_graph::LoopScoreInfo
• current_one_body_energy() : core::pack::interaction_graph::SimpleNode
• current_rot_index() : core::pack::annealer::SimAnnealerBase
• current_rotamer_coords() : core::pack::rotamer_set::ContinuousRotamerSet
• CustomAtomPairEnergy() : core::scoring::methods::CustomAtomPairEnergy
• cut_bond() : core::chemical::Bond
• cut_bond_neighbor() : core::chemical::ResidueType , core::conformation::Residue
• cut_edge() : core::kinematics::FoldTree
• cut_random_edge() : core::kinematics::FoldTree
• cutoff() : core::scoring::CenHBPotential
• cutoff_lower() : core::scoring::func::FadeFunc
• cutoff_upper() : core::scoring::func::FadeFunc
• cutpoint() : core::kinematics::FoldTree
• cutpoint_by_jump() : core::kinematics::FoldTree
• cutpoint_map() : core::kinematics::FoldTree
• cutpoint_open_in_full_model() : core::pose::full_model_info::FullModelInfo
• cutpoints() : core::kinematics::FoldTree
• cuttable() : core::environment::FoldTreeSketch
• cycle() : core::environment::FoldTreeSketch
• cyclic_oxygen() : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_index() : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_name() : core::chemical::carbohydrates::CarbohydrateInfo