- c -

• c : core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::fiber_diffraction::FiberDiffractionOptions , core::scoring::saxs::FastSAXSEnergy
• c0 : core::scoring::etable::CubicPolynomial
• C0_ : core::scoring::constraints::BigBinConstraint , core::scoring::etable::coulomb::Coulomb
• c0_ : core::scoring::FACTSRsdTypeInfo
• c1 : core::scoring::etable::CubicPolynomial
• C1_ : core::scoring::constraints::BigBinConstraint , core::scoring::etable::coulomb::Coulomb
• c1_ : core::scoring::FACTSRsdTypeInfo
• c1prime_index_ : core::chemical::rna::RNA_ResidueType
• c2 : core::scoring::etable::CubicPolynomial
• C2_ : core::scoring::etable::coulomb::Coulomb
• c2_ : core::scoring::FACTSRsdTypeInfo
• c2f : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• c2i : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• c2i_ : core::scoring::PoissonBoltzmannPotential
• c2prime_c3prime_bond_length_ : core::scoring::dna::DNATorsionPotential
• c2prime_c3prime_dist_harm_func_ : core::scoring::dna::DNATorsionPotential
• c2prime_c3prime_sd_ : core::scoring::dna::DNATorsionPotential
• c2prime_index_ : core::chemical::rna::RNA_ResidueType
• c3 : core::scoring::etable::CubicPolynomial
• c3_ : core::scoring::FACTSRsdTypeInfo
• c3prime_c2prime_c1prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• c3prime_c2prime_c1prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• c4prime_c3prime_c2prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• c4prime_c3prime_c2prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• c4prime_index_ : core::chemical::rna::RNA_ResidueType
• c4prime_o4prime_c1prime_angle_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_angle_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_angle_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_bond_angle_ : core::scoring::rna::RNA_SugarCloseEnergy
• C_ : core::pose::CrystInfo , core::scoring::BB_Pos
• c_ : core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::fiber_diffraction::KromerMann
• C_ : core::scoring::func::KarplusFunc , core::scoring::func::PeriodicFunc
• c_alpha_index_ : core::scoring::disulfides::DisulfideAtomIndices
• C_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint
• c_beta_index_ : core::scoring::disulfides::DisulfideAtomIndices
• C_bins : core::scoring::dna::DirectReadoutPotential
• C_gbest_ : core::optimization::ParticleSwarmMinimizer
• C_index_ : core::scoring::BB_Pos
• C_inertia_end_ : core::optimization::ParticleSwarmMinimizer
• C_inertia_start_ : core::optimization::ParticleSwarmMinimizer
• C_lbest_ : core::optimization::ParticleSwarmMinimizer
• C_N_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• C_pbest_ : core::optimization::ParticleSwarmMinimizer
• C_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• CA1_ : core::scoring::constraints::BigBinConstraint
• CA2_ : core::scoring::constraints::BigBinConstraint
• CA_ : core::scoring::BB_Pos
• CA_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint
• ca_cprev_n_h_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• CA_index_ : core::scoring::BB_Pos
• CA_MASK : core::scoring::electron_density::ElectronDensity
• ca_nnext_c_o_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• CA_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cacbcb_angle_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• CaCbCb_angle_scores_ : core::scoring::disulfides::CaCbCb_Angle_Func
• cacbcbca_dihedral_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• CaCbCbCa_dihedral_scores_ : core::scoring::disulfides::CaCbCbCa_Dihedral_Func
• cache_ : core::fragment::Frame
• cache_remarks_ : core::io::silent::SilentStruct
• cached_pose_by_state_ : core::scoring::methods::PoissonBoltzmannEnergy
• cached_tries_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• calc_freq_temp : core::pack::annealer::SimAnnealerBase
• calc_rot_freq_ : core::pack::annealer::SimAnnealerBase
• calcenergy : core::scoring::APBSConfig , core::scoring::APBSConfig::I_PARAM
• calcenergy_ : core::scoring::PoissonBoltzmannPotential
• calcforce : core::scoring::APBSConfig::I_PARAM
• calculate_suiteness_bonus_ : core::scoring::rna::RNA_SuitePotential
• 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::SigmoidWeightedCenList< T >
• calculated_hpatch_deltaE_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculated_surface_deltaE_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• calculators_ : core::pose::metrics::CalculatorFactory
• canonical_aas_to_keep_ : core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• carbohydrate_info_ : core::chemical::ResidueType
• carbohydrate_residue_type_base_names : core::io::pdb::FileData
• carbon_atom : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• carbon_donors_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• carbon_hbond_parameter_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• carbon_hbond_potential_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::ScoringManager
• carbon_types : core::scoring::etable::Etable
• careful_base_pair_classifier_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• cart_resl_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• cart_size_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• cartbonded_ang_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_improper_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_len_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_linear_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_proton_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_tors_ : core::scoring::methods::EnergyMethodOptions
• cartesian_ : core::pack::RTMin
• cases_ : core::chemical::Patch
• cavballs : core::scoring::packstat::CavityBallCluster , core::scoring::packstat::SasaResult
• CB_ : core::scoring::BB_Pos
• cb_angle_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• CB_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint
• CB_CA_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cb_dist_cut_ : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• cb_distance_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• CB_force_constant_ : core::scoring::constraints::BackboneStubLinearConstraint
• CB_index_ : core::scoring::BB_Pos
• CB_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cbeta12_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cbeta6_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cbeta_den12_ : core::scoring::EnvPairPotential
• cbeta_den6_ : core::scoring::EnvPairPotential
• cbsg_dihedral_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• CC_aacen : core::scoring::electron_density::ElectronDensity
• CC_cen : core::scoring::electron_density::ElectronDensity
• CC_pat : core::scoring::electron_density::ElectronDensity
• ccenter : core::scoring::APBSConfig
• CCs : core::scoring::electron_density::ElectronDensity
• ccw : core::scoring::packstat::Event , core::scoring::packstat::trace
• ccw_angle : core::scoring::packstat::Event
• cd_1b_methods_ : core::scoring::ScoreFunction
• cd_2b_intrares_ : core::scoring::ScoreFunction
• cd_2b_methods_ : core::scoring::ScoreFunction
• cd_lr_2b_methods_ : core::scoring::ScoreFunction
• cdf_ : core::scoring::Ramachandran
• cdf_by_torsion_bin_ : core::scoring::Ramachandran
• cell_a_ : core::conformation::symmetry::SymmData
• cell_alfa_ : core::conformation::symmetry::SymmData
• cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cell_b_ : core::conformation::symmetry::SymmData
• cell_beta_ : core::conformation::symmetry::SymmData
• cell_c_ : core::conformation::symmetry::SymmData
• cell_dimensions : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cell_gamma_ : core::conformation::symmetry::SymmData
• cell_volume : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cellAngles : core::scoring::electron_density::ElectronDensity
• cellDimensions : core::scoring::electron_density::ElectronDensity
• cen_cfg_file_ : core::scoring::saxs::SAXSEnergy
• cen_dist10_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_plus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist12_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist12_pad_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist12_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist12_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_plus : core::scoring::EnvPairPotential
• cen_dist12_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist5_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_plus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist6_pad : core::scoring::EnvPairPotential
• cen_dist6_pad_ : core::scoring::membrane::MembraneData
• cen_dist6_pad_hinv : core::scoring::EnvPairPotential
• cen_dist6_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist6_pad_plus : core::scoring::EnvPairPotential
• cen_dist6_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist7_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_plus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist_cutoff2 : core::scoring::EnvPairPotential
• cen_dist_cutoff_12_pad : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• cen_distance_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• cen_disulfide_potential_ : core::scoring::ScoringManager
• cen_hb_potential_ : core::scoring::ScoringManager
• cen_rot_pair_potential_ : core::scoring::ScoringManager
• cenpack_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cenpack_log_ : core::scoring::EnvPairPotential
• center : core::chemical::rna::GaussianParameter , core::scoring::APBSConfig , core::scoring::packstat::CavityBallCluster
• center_ : core::conformation::UltraLightResidue , core::id::NamedStubID , core::id::StubID , core::scoring::hbonds::HBondEnergy , core::scoring::MembraneEmbed
• center_of_mass_ : core::scoring::rna::RG_Energy_RNA
• centerOfMass : core::scoring::electron_density::ElectronDensity
• centers : core::scoring::packstat::PosePackData
• centers_ : core::scoring::packstat::PackingScore , core::scoring::rna::RNA_SuitePotential
• central_atoms_to_score_ : core::scoring::methods::MMBondAngleEnergy , core::scoring::mm::MMBondAngleResidueTypeParamSet
• centroid_ : core::import_pose::ImportPoseOptions
• centroid_dist_scores_ : core::scoring::disulfides::Cen_Distance_Func
• cfac : core::scoring::APBSConfig
• cglen : core::scoring::APBSConfig
• ch1_begin_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch1_end_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch2_begin_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch2_end_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain : core::io::raw_data::DisulfideFile::ResNum , core::scoring::packstat::SimplePDB_Atom
• chain1_ : core::scoring::motif::ResPairMotif
• chain1_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• chain1_letter_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain1_number_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain2_ : core::scoring::motif::ResPairMotif
• chain2_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• chain2_letter_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain2_number_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain_ : core::conformation::Residue , core::fragment::AnnotatedFragData , core::pack::task::operation::ChainIs , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::scoring::methods::D2H_SA_Energy
• chain_endings_ : core::conformation::Conformation , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_strings_ : core::pack::task::residue_selector::ChainSelector
• chainID : core::io::pdb::AtomInformation , core::io::pdb::ResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• chainID1 : core::io::pdb::LinkInformation
• chainID2 : core::io::pdb::LinkInformation
• chains : core::io::pdb::FileData , core::scoring::PQR
• chains_ : core::io::silent::SilentStruct
• chains_whose_residues_are_separate_chemical_entities_ : core::io::pdb::FileDataOptions
• changed_ : core::scoring::FACTSResidueInfo
• changed_residues_ : core::kinematics::ResidueCoordinateChangeList
• charge : core::scoring::PQR
• charge_ : core::chemical::AddAtom , core::chemical::Atom , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::SetAtomicCharge , core::chemical::SetFormalCharge , core::scoring::elec::ElecAtom
• charged_ : core::pack::task::operation::ResidueTypeFilter , core::scoring::FACTSRsdTypeInfo
• charged_chains_ : core::scoring::methods::PoissonBoltzmannEnergy
• charged_residues_ : core::scoring::methods::PoissonBoltzmannEnergy
• charged_residues_map_ : core::scoring::methods::PBLifetimeCache
• check_if_residues_are_Ctermini_ : core::io::pdb::FileDataOptions
• check_if_residues_are_Ntermini_ : core::io::pdb::FileDataOptions
• CHEMICAL : core::kinematics::Edge
• chemical_name_ : core::chemical::Element
• chemical_symbol_ : core::chemical::Element
• chgm : core::scoring::APBSConfig::I_PARAM
• chi : core::pack::dunbrack::ChiSet
• chi1_ : core::scoring::motif::ResPairMotif
• chi2 : core::scoring::saxs::FastSAXSEnergy
• chi2_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::motif::ResPairMotif
• chi_ : core::conformation::Residue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::RotamerExplosion , core::scoring::motif::Xfres
• chi_2_proton_chi_ : core::chemical::ResidueType
• chi_atoms_ : core::chemical::ResidueType
• chi_atoms_indices_ : core::chemical::ResidueType
• chi_clones_ : core::conformation::symmetry::SymmetryInfo
• CHI_energy_function_ : core::scoring::ScoringManager
• chi_follows_ : core::conformation::symmetry::SymmetryInfo
• chi_mean_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_north_potential_guanosine_ : core::scoring::rna::RNA_TorsionPotential
• chi_north_potential_others_ : core::scoring::rna::RNA_TorsionPotential
• 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_potential_syn_guanosine_bonus_ : core::scoring::rna::RNA_TorsionPotential
• chi_purine_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_purine_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_pyrimidine_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_pyrimidine_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_rmsd_ : core::scoring::motif::MotifHit
• chi_rotamers_ : core::chemical::ResidueType
• chi_sample_level_ : core::pack::task::EX
• chi_sd_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_south_potential_guanosine_ : core::scoring::rna::RNA_TorsionPotential
• chi_south_potential_others_ : core::scoring::rna::RNA_TorsionPotential
• chi_start_for_active_residue_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• chi_torsions_ : core::io::silent::RNA_SilentStruct
• chidev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• chidevpen_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• children : core::kinematics::Node
• chimean_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• chino_ : core::chemical::AddChi , core::chemical::AddChiRotamer , core::chemical::AddProtonChi , core::chemical::RedefineChi
• chiral_equivalent_name_ : core::chemical::ResidueType
• chisd_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• Ci_ : core::scoring::FACTSResidueInfo
• ci_1b_methods_ : core::scoring::ScoreFunction
• ci_2b_intrares_ : core::scoring::ScoreFunction
• ci_2b_methods_ : core::scoring::ScoreFunction
• ci_lr_2b_methods_ : core::scoring::ScoreFunction
• ciBR_only_ : core::pack::annealer::FASTERAnnealer
• cif_files_ : core::scoring::cryst::PhenixInterface
• circle : core::scoring::packstat::Event , core::scoring::packstat::trace
• circles_ : core::scoring::packstat::LeeRichards , core::scoring::packstat::Slice
• cis_chi4_mean_ : core::scoring::methods::ProClosureEnergy
• cis_chi4_sd_ : core::scoring::methods::ProClosureEnergy
• cis_omega_ : core::sequence::ABEGO
• CIS_OMG_LOWER_RANGE : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• CIS_OMG_UPPER_RANGE : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• cis_packed_rotno_2_sorted_rotno_ : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• cis_rotamers_ : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• CIS_UPPER_TRANS_LOWER_SPLIT : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• clash_check_ : core::scoring::motif::ResPairMotifQuery
• classification_ : core::io::pdb::HeaderInformation
• classifier : core::pose::rna::RNA_SuiteInfo
• cluster_ : core::scoring::packstat::CavityBall
• cluster_min_volume : core::scoring::packstat::SasaOptions
• coarse_centering_mode : core::scoring::APBSConfig::I_PARAM
• COEF_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• coeff_grad_x : core::scoring::electron_density::ElectronDensity
• coeff_grad_y : core::scoring::electron_density::ElectronDensity
• coeff_grad_z : core::scoring::electron_density::ElectronDensity
• coeffs_density_ : core::scoring::electron_density::ElectronDensity
• com : core::scoring::methods::RG_MinData
• comatms : core::scoring::elec::ElecGroup
• COMM_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• commands_ : core::pack::task::ResfileContents
• comment_lines_ : core::io::silent::SilentFileData
• comments_ : core::io::rna::RDAT , core::sequence::SequenceAlignment
• COMMIT_LIMIT_BETWEEN_UPDATES : 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::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• component_bounds_ : core::conformation::symmetry::SymmetryInfo
• component_membership_ : core::pack::interaction_graph::InteractionGraphBase
• components_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• compound_in_progress_ : core::io::pdb::HeaderInformation
• compounds_ : core::io::pdb::HeaderInformation
• compprob_ : core::scoring::packstat::PackingScore
• computed_ : core::scoring::DenseEnergyContainer , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::OneToAllEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedEnergyContainer , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator
• concave : core::scoring::sc::_RESULTS
• conf_ : core::environment::DofPassport , core::pose::PDBInfo
• confidence_ : core::fragment::SecondaryStructure
• config : core::scoring::APBSWrapper
• config_filename_ : core::scoring::PoissonBoltzmannPotential
• conformation : core::conformation::signals::ConnectionEvent , core::conformation::signals::GeneralEvent
• conformation_ : core::conformation::membrane::MembraneInfo , core::pose::Pose , core::scoring::func::ConformationXYZ
• conformation_obs_hub_ : core::pose::Pose
• conformation_pt_ : core::scoring::constraints::ConstraintSet
• conformer_set_ : core::chemical::ResidueType
• conformers_ : core::chemical::RingConformerManager
• conjug_ : core::chemical::Bond
• conjugated_ : core::chemical::gasteiger::GasteigerAtomTypeData
• conn_id_ : core::chemical::ResConnID
• connect_atom_ : core::chemical::AddConnect
• connect_map_ : core::conformation::Residue
• connected_by_twobonds_ : core::scoring::methods::GoapRsdType
• connection_atom_sets_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_distance_ : core::scoring::etable::etrie::CountPairData_1_1
• connection_distances_ : core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3
• connection_gaps_ : core::scoring::etable::etrie::TrieCountPairGeneric
• connection_index_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_obs_hub_ : core::conformation::Conformation
• connection_theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_use_theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connections_to_residues_ : core::conformation::Residue
• conservation_ : core::pose::datacache::PositionConservedResiduesStore
• constraint_set_ : core::pose::Pose , core::scoring::constraints::CstEnergyContainer
• constraints_ : core::scoring::constraints::Constraints , core::scoring::constraints::CstMinimizationData
• constraints_ready_ : core::scoring::dna::DNATorsionEnergy
• contains_carbohydrate_residues_ : core::conformation::Conformation
• context_dependent_ : core::scoring::elec::FA_GrpElecEnergy
• context_derivative_empty_ : core::scoring::FACTSPoseInfo
• context_graphs_ : core::scoring::Energies
• context_graphs_required_ : core::scoring::ScoreFunctionInfo
• context_minstrength_ : core::scoring::elec::FA_GrpElecEnergy
• contiguous_monomers_ : core::conformation::symmetry::SymmetryInfo
• continuous_ : core::scoring::methods::GoapEnergy
• conventional_chains_ : core::pose::full_model_info::FullModelParameters
• conventional_numbering_ : core::pose::full_model_info::FullModelParameters
• convex : core::scoring::sc::_RESULTS
• coor : core::scoring::sc::_DOT
• coordinate_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• coords_ : core::conformation::UltraLightResidue , core::fragment::BBTorsionSRFD , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::scmin::ResidueAtomTreeCollectionMomento , core::pose::MiniPose , core::pose::UnrecognizedAtomRecord , core::sequence::Cell
• copy_dofs_info_ : core::pose::copydofs::CopyDofs
• COradius2_ : core::scoring::FACTSRsdTypeInfo
• cos_flipped_ANGLE_CUTOFF_HIGH : core::scoring::methods::LK_SigmoidalFunc
• cos_flipped_ANGLE_CUTOFF_LOW : core::scoring::methods::LK_SigmoidalFunc
• cos_r_cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• 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
• cosRcellAngles : core::scoring::electron_density::ElectronDensity
• coulomb_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::GroupElec , core::scoring::rna::StackElecEnergy
• count_ : core::scoring::motif::ResPairMotif
• count_viols_ : core::scoring::func::CountViolFunc , core::scoring::func::SkipViolFunc
• count_water_ : core::pack::task::residue_selector::NumNeighborsSelector
• couplings_ : core::pack::rotamer_set::RotamerCouplings
• cp_data_ : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA >
• cp_half : core::scoring::etable::count_pair::CountPairFunction
• CP_parameters : core::chemical::RingConformer
• cpfxn_weight_ : core::scoring::elec::GroupElec
• cprev_n_bond_length_params_ : core::scoring::methods::ResidueCartBondedParameters
• creator_map_ : core::pack::task::residue_selector::ResidueSelectorFactory
• cross_val_ : core::scoring::ProQPotential
• crossover_ : core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::etrie::TrieCountPairGeneric
• crystinfo : core::io::pdb::FileData
• crystinfo_ : core::pose::PDBInfo
• CS_RAD_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• CS_RCY_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• CS_RGU_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• CS_URA_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• cs_verbose_mode_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• csa_score_ : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• CSAerr_ : core::scoring::CSA
• CSAval_ : core::scoring::CSA
• CSAval_computed_ : core::scoring::CSA
• csf_cbang1_ : core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::CBSG_Dihedral_Func
• csf_cbang1a_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang1b_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang2_ : core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::CBSG_Dihedral_Func
• csf_cbang2a_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang2b_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang3_ : core::scoring::disulfides::CBSG_Dihedral_Func
• cst_ : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• cst_graph_ : core::scoring::constraints::CstEnergyContainer
• cst_max_seq_sep_ : core::scoring::methods::EnergyMethodOptions
• cst_score_types_ : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• cst_set_ : core::pose::full_model_info::FullModelParameters
• cst_set_revision_id_ : core::scoring::constraints::CstEnergyContainer
• cst_string_ : core::pose::full_model_info::FullModelParameters
• cst_types_ : core::scoring::constraints::ConstraintFactory
• ctab_mode_ : core::chemical::sdf::MolWriter
• cubes : core::scoring::packstat::Octree2D
• curr_ : core::chemical::AutomorphismIterator
• curr_bg_bg_exhpobeolap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• curr_dots_cache_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• curr_in_recent_history_ : core::pack::annealer::FASTERAnnealer
• curr_memory_for_rpes_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• curr_sc_centroid_ : core::pack::interaction_graph::SimpleNode
• curr_sc_radius_ : core::pack::interaction_graph::SimpleNode
• curr_state_energy_ : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• curr_state_exolap_hphobes_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G >
• curr_state_exp_hphobes_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , 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_one_body_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• curr_state_sparse_mat_info_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• curr_state_total_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• curr_state_total_hASA_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• curr_state_two_body_energies_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• current_distance_ : core::scoring::loop_graph::LoopScoreInfo
• current_energy_ : core::pack::interaction_graph::SimpleEdge
• current_filename_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream
• current_index_ : core::import_pose::pose_stream::MetaPoseInputStream
• current_input_stream_ : core::import_pose::pose_stream::MetaPoseInputStream
• current_maximum_id_ : core::environment::EnvCore
• current_n_ : core::import_pose::pose_stream::ExtendedPoseInputStream
• current_one_body_energy_ : core::pack::interaction_graph::SimpleNode
• current_pose_loop_score_info_ : core::scoring::loop_graph::LoopGraph
• current_position_ : core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• current_residue_ : core::pack::interaction_graph::SimpleNode
• current_rot_index_ : core::pack::annealer::SimAnnealerBase
• current_rotamer_copy_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• current_state_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• current_state_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• current_state_rotamer_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• current_struct_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream
• current_to_pick_ : core::pack::annealer::RotamerAssigningAnnealer
• custom_variant_types_ : core::chemical::ResidueProperties
• cut_bond_ : core::chemical::Bond
• cut_bond_neighbor_ : core::chemical::ResidueType
• cut_bond_neighbor_indices_ : core::chemical::ResidueType
• cut_off_born_radius_ : core::scoring::FACTSPotential
• cutoff_cst_score_ : core::scoring::constraints::KofNConstraint
• cutoff_lower_ : core::scoring::func::FadeFunc
• cutoff_lr_ : core::scoring::CenHBPotential
• cutoff_sr_ : core::scoring::CenHBPotential
• cutoff_upper_ : core::scoring::func::FadeFunc
• cutpoint_ : core::kinematics::FoldTree
• cutpoint_map_ : core::kinematics::FoldTree
• cw_angle : core::scoring::packstat::Event
• cyclic_oxygen_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_index_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_name_ : core::chemical::carbohydrates::CarbohydrateInfo