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Class Hierarchy

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This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 12345678]
 Ccore::scoring::sc::_ATOM_RADIUS
 Ccore::scoring::sc::_DOT
 Cprotocols::abinitio::_HashEntry
 Cprotocols::abinitio::_MergableEntries
 Ccore::scoring::sc::_PROBE
 Ccore::scoring::sc::_RESULTS
 CA
 CA
 CA
 CAOf residues
 CA
 Cprotocols::mean_field::AAProb
 Ccore::sequence::ABEGOAbego elments
 Cprotocols::abinitio::AbrelaxApplicationApplication level code for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT
 Ccore::chemical::AcceptorAtomFilterThe filter responsible for obtaining all acceptor atoms
 Ccore::conformation::AddEdgeVisitor< Vertex, Edge >
 Ccore::chemical::AdductDescription of optional single-atom residue adducts
 Cprotocols::cluster::calibur::AdjacentList
 Ccore::io::mmtf::ai_cmpSimple comparator for AtomInformation when grouping by residue/grp
 Ccore::sequence::AlignerFactory
 Cprotocols::sewing::hashing::AlignmentFGMSettings
 Cprotocols::comparative_modeling::AlignmentSet
 Cprotocols::sewing::hashing::AlignmentSettings
 CAlternating
 Cprotocols::abinitio::AlternativePairings
 Ccore::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
 Ccore::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >
 CAn
 CAn
 Cprotocols::sparta::ANN
 Ccore::pack::annealer::AnnealerFactory
 Cprotocols::antibody_legacy::AntibodyAntibody definition
 Cprotocols::antibody::AntibodyNumbering
 Ccore::chemical::APolarHydrogenFilterThe filter responsible for all apolar hydrogens
 Cprotocols::denovo_design::connection::AreConnectablePredicate
 Ccore::chemical::AromaticAtomFilterThe filter responsible for all aromatic atoms
 Ccore::scoring::packstat::Array2D
 Cprotocols::legacy_sewing::AssemblyFactoryAn Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher
 Cprotocols::sewing::requirements::AssemblyRequirementInterface for making Requirements that deal with Assemblies
 Cprotocols::sewing::scoring::AssemblyScorerInterface for making Requirements that deal with Assemblies
 Ccore::scoring::hbonds::AssignmentScaleAndDerivVectIDClasses (that probably shouldn't be in here!!! ) ///
 Ccore::chemical::orbitals::AssignOrbitals
 CASTVisitor
 Cprotocols::ligand_docking::ga_ligand_dock::atmInfo
 Ccore::chemical::Atom
 Ccore::conformation::Atom
 Ccore::pose::rna::Atom_Bin
 Cprotocols::simple_moves::AtomHash
 Cprotocols::simple_moves::AtomHashNode
 Ccore::chemical::AtomICoorA basic class containing info of internal coordinates needed for building an atom within a ResidueType
 Ccore::id::AtomIDAtom identifier class. Defined by the atom number and the residue number
 Ccore::id::AtomID_Map< T >Map from Atom identifiers to contained values class
 Ccore::id::AtomID_Map< AtomID >
 Ccore::id::AtomID_Map< bool >
 Ccore::id::AtomID_Map< core::id::AtomID >
 Ccore::id::AtomID_Map< core::Real >
 Ccore::id::AtomID_Map< core::scoring::packstat::LR_AtomData >
 Ccore::id::AtomID_Map< core::scoring::packstat::LR_MP_AtomData >
 Ccore::id::AtomID_Map< core::Size >
 Ccore::id::AtomID_Map< numeric::xyzVector< core::Real > >
 Ccore::id::AtomID_Map< Real >
 Ccore::id::AtomID_Map< Size >
 Ccore::id::AtomID_Map< tree::AtomOP >
 Ccore::id::AtomID_Map< utility::vector1< Real > >
 Ccore::id::AtomID_Map< utility::vector1< Size > >
 Ccore::id::AtomID_Map< utility::vector1< utility::vector1< Real > > >
 Ccore::id::AtomID_Map< Vector >
 Cprotocols::sic_dock::AtomIDHashFunction
 Ccore::scoring::hbonds::graph::AtomInfo
 Ccore::io::AtomInformation
 Ccore::scoring::AtomNeighborAtom-atom neighborlist object
 Cprotocols::abinitio::abscript::AtomPack
 Cprotocols::ligand_docking::rdf::AtomPairDataSimple struct for storing information needed to compute an RDF interaction
 Ccore::scoring::etable::AtomPairEnergy
 Cprotocols::ligand_docking::ga_ligand_dock::AtomPropertiesAtom properties important in constraint generation
 Ccore::scoring::packstat::AtomRadiusMap
 Ccore::pose::PDBInfo::AtomRecordInternal struct for storing PDB atom related information
 Ccore::scoring::custom_pair_distance::atoms_and_func_struct
 Ccore::io::nmr::AtomSelection
 Ccore::chemical::AtomTypeBasic atom type
 CAtomTypeDataHybridization and bond geometry data, which is used in Atom
 Ccore::kinematics::AtomWithDOFChangeSimple class for use in output-sensitive refold subroutine
 Cprotocols::loophash::BackboneDB
 Cprotocols::loophash::BackboneSegment
 Ccore::pack::interaction_graph::BackgroundNode< V, E, G >A node which is not changing type or rotamer throughout a simulation
 Ccore::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >An edge between a background node and a first class node
 Cprotocols::backrub::BackrubSegmentClass for holind information about individual backrub segments
 CBadInput
 Cprotocols::jd2::archive::BaseArchiveManagerArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY
 Cprotocols::stepwise::modeler::rna::rigid_body::BaseBin
 Ccore::import_pose::libraries::BasePairType
 Cstd::basic_string< Char >STL class
 Cprotocols::rpc::BasicInit
 Cprotocols::legacy_sewing::Basis
 Cprotocols::sewing::hashing::BasisMapGeneratorGiven a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover
 Cprotocols::jd2::archive::BatchBatch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive
 Ccore::scoring::BB_Pos
 Cprotocols::fldsgn::topology::BB_Pos
 Cprotocols::loophash::BBData
 Ccore::pack::dunbrack::BBDepNRChiSample< P >P for precision
 Ccore::pack::dunbrack::BBDepNRChiSample< Real >
 Ccore::pack::dunbrack::BBDepScoreInterpData< N >
 Cprotocols::loophash::BBExtraData
 Ccore::pack::dunbrack::BBIndNRChiSample< P >
 Cbinary_function
 CBinaryExpression
 Ccore::pack::guidance_scoreterms::sap::BlockParam
 Ccore::sequence::Blosum62Map
 Cprotocols::boinc::Boinc
 Cprotocols::boinc::BoincSharedMemory
 Ccore::chemical::BondBasic chemical Bond
 Ccore::chemical::sdf::BondData
 Ccore::id::BondIDTwo more classes, temporary for testing purposes
 Ccore::scoring::BondOrderParser
 Ccore::fragment::picking_old::concepts::Book< Pages >Forward declaration for Book
 Ccore::fragment::picking_old::concepts::Book< core::fragment::picking_old::vall::VallResidues >
 Ccore::fragment::picking_old::concepts::Book< VallResidues >
 Cprotocols::match::Bool3DGridKinemageWriter
 Cprotocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
 Cprotocols::branch_angle::BranchAngleOptimizer
 Cprotocols::branch_angle::BranchCoef1Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors
 Cprotocols::branch_angle::BranchParam1Class to store bond angle energy parameters around a single atom atom with three bonded neighbors
 Cprotocols::environment::EnvClaimBroker::BrokerResult
 Ccore::io::serialization::BUFFER
 Ccore::pack::rotamer_set::BumpSelector
 CCacheableData
 Ccore::pose::datacache::CacheableDataType
 Ccore::fragment::CacheWrapper< T, XCacheUnit >
 Ccore::fragment::CacheWrapper< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::GunnTuple > >
 Ccore::fragment::CacheWrapper< T, MapCacheUnit< T > >
 Ccore::fragment::CacheWrapper< T, VectorCacheUnit< T > >
 Ccore::pose::metrics::CalculatorFactory
 Cprotocols::nonlocal::SmoothPolicy::Candidate
 Cprotocols::cartesian::CartesianAtom
 Ccore::scoring::packstat::CavityBall
 Ccore::scoring::packstat::CavityBallCluster
 Cprotocols::sic_dock::CBScoreVisitor
 Cprotocols::pockets::CCluster@ Cluster of exemplar points
 Cprotocols::pockets::CClusterSet@ Set of clusters of exemplar points
 Cprotocols::antibody::CDRDBPose
 Cprotocols::antibody::CDRDBSequence
 Ccore::scoring::disulfides::CentroidDisulfideEnergyComponentsStorage for Disulfide Energy Terms
 Ccore::pack::dunbrack::cenrot::CentroidRotamerSampleDataSimple class storing all the data for one centroid-rotamer well
 Cprotocols::make_rot_lib::CentroidRotNum
 Cprotocols::pose_length_moves::Chain
 Ccore::util::ChainbreakUtil
 Ccore::pack::task::operation::ResiduePDBIndexIs::ChainPos
 Cprotocols::constel::ChainTerm
 Cprotocols::qsar::scoring_grid::ChargeAtomVery light representation of an atom that is just a charge and a cartesian space position
 Ccore::sequence::CharPairHash
 Cprotocols::cryst::CheshireCellA struct used by spacegroup.cc and its helper functions
 Ccore::scoring::carbohydrates::CHIDihedralSamplingDataStruct for CHI-based dihedral sampling
 Cprotocols::ligand_docking::ga_ligand_dock::ChiInfo
 Cprotocols::pose_creation::SliceToMiniProteinMover::Chunk
 Cprotocols::jd3::chunk_library::ChunkLibraryPreliminaryLarvalJob
 Ccore::scoring::packstat::Circle
 Ccore::io::CisPeptideInformation
 Cprotocols::topology_broker::ClaimerMessage
 Cprotocols::features::clique_saver
 Ccore::scoring::sc::CloserToAtomA small struct to report which of two atoms is closer to a given atom:
 Cprotocols::cluster::Cluster
 Cprotocols::stepwise::legacy::modeler::rna::Cluster_Member
 Cprotocols::toolbox::ClusterBase
 Cprotocols::antibody::clusters::ClusterDataHolds data for each cluster type
 Cprotocols::mpi_refinement::Clusterer
 Cprotocols::cluster::calibur::Clustering
 Cprotocols::toolbox::ClusterOptions
 Cprotocols::topology_broker::CmdLineData
 Cprotocols::qsar::ColorGradient
 Cprotocols::stepwise::modeler::rna::Combine_Tags_Info
 Cprotocols::environment::ComparatorA brief comparator object initialized with the correct strength accessor for reuse of setup_passports
 Cprotocols::stepwise::modeler::rna::rigid_body::compare_base_bin
 Cprotocols::hbnet::compare_by_x
 Cprotocols::stepwise::modeler::rna::rigid_body::compare_int_pair
 Cprotocols::pockets::ComparisonGrid@
 Cprotocols::jd3::CompletedJobOutputEach Job will return a JobStatus and a list of JobSummary/JobResult pairs. A pair's index in th job_results vector is used as its identifier for when the JobResult is used as input for another job, or when it is to be output by the JobQueen
 Cprotocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessageCompletionMessage(s) are send to the ArchiveManager whenever more than nr_notify decoys have been finished / or when the full batch is finished
 CComputes
 Ccore::conformation::signals::ConnectionEventSignal a change in the connection with a Conformation object, e.g. destruction or transfer
 Ccore::io::raw_data::RawFileData::const_iteratorConst_iterator class for RawFileData container
 Ccore::io::silent::SilentFileData::const_iteratorConst_iterator class for SilentFileData container
 Cprotocols::md::Constraint
 Cprotocols::fold_from_loops::constraint_generator::ConstraintConditions
 Cprotocols::ligand_docking::ga_ligand_dock::ConstraintInfoConstraint information about AtomProperties and/or Pharmacophores
 Cprotocols::contact_map::ContactSimple class representing a contact between two atoms
 Cprotocols::sewing::data_storage::ContactDescription
 Cprotocols::contact_map::ContactPartnerSimple class that holds the information on an atom involved in a contact
 Cprotocols::normalmode::ContactStruct
 Ccore::scoring::ContextGraphFactory
 Ccore::optimization::ConvergenceTest
 Ccore::chemical::CopyEdge< Graph1, Graph2 >
 Ccore::chemical::CopyVertex< Graph1, Graph2 >
 Cprotocols::sic_dock::CorrectionVisitor
 Ccore::scoring::etable::etrie::CountPairData_1_1
 Ccore::scoring::etable::etrie::CountPairData_1_2
 Ccore::scoring::etable::etrie::CountPairData_1_3
 Ccore::scoring::etable::etrie::CountPairDataGeneric
 Ccore::scoring::etable::count_pair::CountPairFactory
 Ccore::scoring::elec::CountPairRepMapA class to encapsulate the raw-pointer-based data caching
 Ccore::scoring::trie::CPDataCorrespondence
 CCrossoverBehavior
 Ccore::io::CrystInfo
 Cprotocols::frag_picker::CS2ndShift
 Ccore::scoring::CSA
 Cprotocols::frag_picker::CSTalosIO
 Ccore::chemical::sdf::CtabParserBase
 Cprotocols::denovo_design::movers::CutAndJump
 Cprotocols::environment::claims::CutBiasElement
 Cprotocols::environment::claims::CutElement
 Cprotocols::pockets::PCluster::Cxyz
 Cprotocols::pockets::CCluster::Cxyz
 Ccore::scoring::loop_graph::cycle_printer
 Cprotocols::peptide_deriver::CyclizedPeptideInfo
 Cprotocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfo
 Ccore::scoring::data_struct
 Cprotocols::relax::DatabaseRelaxScriptRepresents a single line of database/sampling/relax_scripts/index.dat
 Cprotocols::canonical_sampling::mc_convergence_checks::DataBuffer
 CDataCache
 CDataMap
 Cprotocols::cluster::DataPointData structure for one input data point for affinity propagation clustering
 Ccore::scoring::DC
 Cprotocols::ddG::ddGData
 Cprotocols::hybridization::DDomainParse
 Cprotocols::hbnet::DecoratedNetworkState
 Ccore::scoring::epr_deer::DEERIO
 Cdefault_dfs_visitor
 Cprotocols::electron_density::DensitySymmInfoScale density map intensities to match a pose's
 Cprotocols::loop_grower::DensSkeleton
 Ccore::optimization::DerivCheckDataPoint
 Cprotocols::peptide_deriver::DerivedPeptideEntry
 Ccore::scoring::DerivVectorPairA glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms
 Ccore::optimization::DescentDirectionAlgorithm
 Cprotocols::pose_creation::MakeJunctionsMover::Design
 Ccore::io::sequence_comparation::DesignContrastDesignContrast contains information for comparing the native protein sequence to designed protein sequence. And output the compare resultes to a special formated file which can be used for statistics calculations
 Ccore::pose::signals::DestructionEventSpecial signal that the Pose is getting destroyed
 Cprotocols::hybridization::detailedControlsTagSetting
 CDigraph
 CDirectedEdge
 CDirectedNode
 Cprotocols::indexed_structure_store::DirectSegmentLookup
 Cprotocols::indexed_structure_store::DirectSegmentLookupConfig
 Cprotocols::indexed_structure_store::DirectSegmentLookupResult
 Cprotocols::noesy_assign::FragsToAtomDist::DistanceRecord
 Ccore::scoring::disulfides::DisulfideAtomIndicesThis class is used by the *DisulfideEnergyContainer and the *DisulfidePotential classes to rapidly index into a residue that's known to form a disulfide. For the sake of computing derivatives, there are only three atoms that need to be readily available: CA, CB, and the atom which makes the disulfide bond, either SG or CEN. The DisulfideEnergyContainer is responsible for keeping the indices in one of these objects up-to-date with the residue it is meant to shadow
 Ccore::io::raw_data::DisulfideFileParses and stores a disulfide file
 Ccore::scoring::disulfides::DisulfideMatchingDatabase
 Ccore::scoring::disulfides::DisulfideMatchingEnergyComponentsStorage for Disulfide Energy Terms
 Cprotocols::jumping::DisulfPairing
 Cprotocols::jumping::DisulfTemplate
 Ccore::scoring::dna::DNA_DihedralPotential
 Cprotocols::dna::DNABase
 Cprotocols::dna::DNABasepair
 Cprotocols::dna::DNABasestep
 Cprotocols::dna::DnaNeighbor
 Cprotocols::dna::DnaPosition
 Ccore::optimization::DOF_DataPoint
 Ccore::id::DOF_IDKinematics DOF identifier class
 Ccore::id::DOF_ID_Map< T >Map from Atom DOF identifiers to contained values class
 Ccore::id::DOF_ID_Map< DOF_NodeOP >
 Ccore::id::DOF_ID_Map< id::TorsionID >
 Ccore::id::DOF_ID_RangeKinematics DOF identifier (with range) class
 Cprotocols::environment::claims::DOFElement
 Cprotocols::simple_moves::DOFHistogramRecorder
 Ccore::scoring::constraints::MultiConstraint::dont_copy_constraints
 Ccore::pack::interaction_graph::DotSphereRepresents the sphere of dots on the vdW surface of an atom, for use in the LeGrand and Merz method of calculating SASA
 Cprotocols::match::downstream_hit
 Ccore::scoring::dssp::Dssp
 Ccore::pack::dunbrack::DunbrackAAParameterSetA small structure to hold overview parameters about the Dunbrack Libraries
 Ccore::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >Forward declaration; default precision is DunbrackReal
 Ccore::pack::dunbrack::DunbrackRotamerMeanSD< S, N, Real >
 Ccore::pack::dunbrack::DunbrackRotamerSampleData
 CE
 Ccore::kinematics::EdgeSingle edge of the fold_tree
 CEdge
 Ccore::pack::interaction_graph::EdgeBase
 Ccore::optimization::EItemInner class for Genetic Algorithm, hold one population with some additional info
 Ccore::scoring::elec::electrie::ElecAtom
 Ccore::scoring::elec::ElecGroup
 Ccore::scoring::elec::electrie::ElecTrieEvaluator
 Ccore::chemical::ElectronConfigurationDescribes the electron configuration of atoms
 Ccore::scoring::electron_density_atomwise::ElectronDensityAtomwise
 Ccore::scoring::sc::ElectrostaticComplementarityCalculator
 Ccore::scoring::sc::ElectrostaticComplementarityResults
 Ccore::scoring::sc::ElectrostaticSimilarityCalculator
 Ccore::scoring::sc::ElectrostaticSimilarityResults
 Ccore::scoring::EMapVectorA vector for storing energy data, initially all values are 0
 Cprotocols::pose_metric_calculators::EmptyVertexData
 Cenable_shared_from_this
 Cprotocols::pose_metric_calculators::EnergiesData
 Cprotocols::genetic_algorithm::EntityElementsEqual
 Cprotocols::pack_daemon::EntityHistoryLT
 Cprotocols::ligand_docking::ga_ligand_dock::EntropyEstimatorEstimates entropy change by ligand binding using short MC simulation
 Ccore::select::Enumerate1WithSelector
 Cupdate_ResidueType_enum_files.EnumInfo
 Ccore::enzymes::EnzymeDataA structure for storing reaction information for specific virtual enzymes
 Ccore::scoring::epr_deer::EPRSpinLabel
 Ccore::scoring::etable::EtableParamsOnePairEtableParamsOnePair describes all of the parameters for a particular pair of atom types necessary to evaluate the Lennard-Jones and LK solvation energies
 Ccore::scoring::packstat::Event
 CException
 Cprotocols::canonical_sampling::AsyncMPITemperingBase::ExchangeRequest
 Cprotocols::constel::ExcludedFilter
 Cprotocols::cluster::ExemplarData structure for one similarity measurement (s_ik) for affinity propagation clustering
 Ccore::pack::interaction_graph::exposed_hydrophobic_data
 CExpression
 CExpressionCreator
 Ccore::fragment::picking_old::concepts::Extent< PageIterator >Forward declaration for Extent
 Ccore::scoring::etable::ExtraQuadraticRepulsionExtraQuadraticRepulsion class is used to add in extra repulsion for particular atom pairs, if needed, (e.g. for OCbb/OCbb) where the functional form is: fa_rep += (xhi - x)^2 * slope for values of x between xlo and xhi, and fa_rep += (x - xlo ) * extrapolated_slope + ylo where extrapolated slope can be anything, but, to defined a function with continuous derivatives, should be extrapolated_slope = (xhi-xlo)^2*slope. This is the analytical implementation of the "modify_pot" behavior
 Ccore::pack::task::operation::ExtraRotamerSamplingData
 Ccore::scoring::facts::FACTSRsdTypeMapThe FACTSRsdTypeMap is a collection of FACTSRsdTypeInfo for a number of residue types (This is a separate class to shield the raw pointer usage here
 Cprotocols::protein_interface_design::FavorNativeResidue
 Cprotocols::protein_interface_design::FavorNonNativeResidue
 Ccore::io::pdb::Field
 Cprotocols::checkpoint::FileBuffer
 Cprotocols::loophash::FilterBucket
 Cprotocols::constel::FilterByAmphetamineClass to filter out constellations that cannot (putatively) be rescued by amphetamine
 Cprotocols::constel::FilterByHistamineClass to filter out constellations that cannot (putatively) be rescued by histamine
 Cprotocols::constel::FilterByIndoleCOOClass to filter out constellations that cannot (putatively) be rescued by compounds containing indole and a carboxylic group
 Cprotocols::constel::FilterByProxTerm
 Cprotocols::constel::FilterBySASA
 Cprotocols::constel::FilterByTryptamineClass to filter out constellations that cannot (putatively) be rescued by tryptamine
 Cprotocols::stepwise::modeler::rna::Filterer_Count
 Cprotocols::pose_length_moves::FinalRMSDComparator
 Cprotocols::wum::find_SilentStructOPsThis little class is a predicate for finding silent structures in say a vector of silent structures
 Cflat_set
 Cprotocols::flexpack::interaction_graph::FlexbbIGFactory
 Cprotocols::flexpep_docking::FlexPepDockingPoseMetrics
 Cprotocols::noesy_assign::FoldResonance
 Ccore::scoring::saxs::FormFactorManagerSelects a given number of fragments using a quota scheme
 Ccore::fragment::FragFactory
 Ccore::fragment::FragID
 Cprotocols::topology_broker::FragmentContainer
 Ccore::fragment::FragmentIO
 Cprotocols::indexed_structure_store::FragmentLookupResult
 Cprotocols::features::helixAssembly::FragmentPair
 Cprotocols::indexed_structure_store::FragmentSpecification
 Cprotocols::canonical_sampling::DbTrajectoryRecorder::FrameHelper struct used store cached poses
 Cprotocols::trajectory::DbTrajectoryWriter::Frame
 Cprotocols::antibody::FrameWork
 Ccore::scoring::disulfides::FullatomDisulfideEnergyComponents
 Ccore::scoring::disulfides::FullatomDisulfideParams13
 Ccore::import_pose::FullModelPoseBuilder
 Cprotocols::jd3::full_model::FullModelPreliminaryLarvalJob
 Ccore::optimization::func_1d
 Cprotocols::mean_field::jagged_array< T, A >::func_T2< T_2 >
 Ccore::scoring::func::FuncFactory
 CG
 Ccore::optimization::GA_Minimizer
 Cprotocols::ligand_docking::ga_ligand_dock::GADockStageParamsRepresent options for a single "phase" of ligand docking
 Cprotocols::ligand_docking::ga_ligand_dock::GAOptimizerGenetic Algorithm Optimizer called by GALigandDock
 Ccore::chemical::rna::GaussianParameter
 Cprotocols::sparta::GDB
 Ccore::pose::signals::GeneralEventSignals a general change in a Pose
 Ccore::conformation::signals::GeneralEventSignals a general change in a Conformation
 Ccore::scoring::etable::etrie::GenericResidueConnectionData
 Ccore::scoring::GenTorsionParamsParameter set for one torsion angle
 Ccore::io::pose_from_sfr::GeometricRenameIsomorphismCallback
 Ccore::io::pose_from_sfr::GeometricRenameVerticiesEquivalentWill consider two verticies equivalent if they have the same element
 CGraph
 Cprotocols::viewer::GraphicsState
 Ccore::chemical::GraphvizPropertyWriterCallback class for write_graphviz - outputs properties for the nodes and edges
 Ccore::io::pose_from_sfr::GraphvizPropertyWriterCallback class for writing graphviz info
 Cprotocols::ligand_docking::ga_ligand_dock::GridHash3D< T >
 Cprotocols::ligand_docking::ga_ligand_dock::GridHash3D< protocols::ligand_docking::ga_ligand_dock::hbAcc >
 Cprotocols::ligand_docking::ga_ligand_dock::GridHash3D< protocols::ligand_docking::ga_ligand_dock::hbDon >
 Cprotocols::ligand_docking::ga_ligand_dock::GridScorerGrid representation of scorefunction
 Cprotocols::scoring::methods::pcs2::GridSearchIteratorCA
 Cprotocols::seeded_abinitio::GrowPeptidesSegment
 Cprotocols::frag_picker::scores::GunnCost
 Cprotocols::frag_picker::scores::GunnTuple
 Ccore::scoring::Hairpin
 Ccore::scoring::Hairpins
 Ccore::scoring::fiber_diffraction::Hankel
 Cprotocols::match::downstream::hash_upstream_hit
 Cprotocols::sewing::hashing::HasherSettings
 Cprotocols::legacy_sewing::HashResult
 Cprotocols::legacy_sewing::HashValue
 Cprotocols::sewing::hashing::HashValue
 Cprotocols::ligand_docking::ga_ligand_dock::hbAcc
 Ccore::scoring::hbonds::hbtrie::HBAtom
 Ccore::scoring::hbonds::hbtrie::HBCPData
 Ccore::scoring::hbonds::HBDerivAssigner
 Cprotocols::ligand_docking::ga_ligand_dock::hbDon
 Ccore::scoring::hbonds::HBEvalTuple
 Ccore::pack::guidance_scoreterms::approximate_buried_unsat_penalty::HBondBonusOptions
 Cprotocols::constel::HBondCommonA class to hold data structures and functions shared by filters that consider hydrogen bonding
 Ccore::scoring::hbonds::HBondDerivs
 Ccore::scoring::hbonds::graph::HBondInfo
 Ccore::scoring::hbonds::HBondTypeManager
 Ccore::chemical::HeavyAtomFilterThe filter responsible for obtaining all heavy atoms
 Ccore::chemical::HeavyAtomWithHydrogensFilterThe filter responsible for finding heavy atoms with hydrogens
 Ccore::chemical::HeavyAtomWithPolarHydrogensFilterThe filter responsible for obtaining all heavy atoms with polar hydrogens attached to them
 Ccore::scoring::Helices
 Ccore::io::HELIXInformation
 Cprotocols::helix_capper::HelixNCapperMover
 Ccore::pack::interaction_graph::history_queue_structFor storing three peices of associated data describing the recent history structure on a LinearMemNode
 Cprotocols::match::Hit
 Cprotocols::simple_moves::Hit
 Ccore::scoring::packing::HolesParams
 Ccore::scoring::packing::HolesParamsRes
 Ccore::scoring::packstat::HTL_EventX
 Cprotocols::hybridization::HybridizeFoldtreeDynamic
 Ccore::chemical::HydrogenAtomFilterThe filter responsible for all hydrogens
 Ccore::chemical::ICoorAtomIDAtom 's ID in internal coordinates in a ResidueType
 Ccore::chemical::orbitals::ICoorOrbitalData
 Cprotocols::sewing::hashing::IdealContact
 CImplements
 CImplements
 Cprotocols::forge::remodel::RemodelMover::instruction_flags
 Ccore::pack::interaction_graph::InteractionGraphFactory
 Cprotocols::toolbox::InteratomicVarianceMatrix
 Cprotocols::analysis::InterfaceDataAll interface data. Unless otherwise specified, they refer specifically to the interface
 Cprotocols::ligand_docking::ligand_options::InterfaceInfoInfo for each residue- is it part of the interface and if so, what ligands is it near
 Cprotocols::stepwise::modeler::rna::InternalWorkingResidueParameter
 Cprotocols::jumping::IntervalTwo numbers, i.e., jump start end residue, or cut-regions..
 Cprotocols::forge::build::IntervalSimple struct defining a closed interval of residues [left, right] where left <= right
 Ccore::scoring::etable::count_pair::Invoker
 Cprotocols::simple_moves::IonizableResidue
 Cstd::ios_baseSTL class
 Cprotocols::motifs::IRCollection
 Cprotocols::simple_moves::LoggedFragmentMover::Item
 Cprotocols::optimize_weights::IterativeOptEDriver
 Ccore::io::raw_data::RawFileData::iteratorIterator class for RawFileData container
 Ccore::io::silent::SilentFileData::iteratorIterator class for SilentFileData container
 Citerator
 Ccore::kinematics::jacobian::ModuleType1::jacobian_structStruct to pass around all variations of Jacobian matrices fw_dofs is the Jacobian matrix that maps differential torsion angles [rad/s] or [delta rad] on Cartesian reference frame fw_cons is the 6x6 Jacobian matrix that maps virtual (helper, constrained) torsion angles [rad/s] or [delta rad] on Cartesian reference frame fw_all is the 6x6 Jacobian matrix that maps all six torsion angles (real and virtual) [rad/s] or [delta rad] on Cartesian reference frame inv_dofs is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto torsion angles inv_cons is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto virtual torsion angles that represent the modules constraints inv_all is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto all torsion angles (real and virtual)
 Cprotocols::frag_picker::JCouplingIO
 Cprotocols::jd3::JobGenealogist::JGJobNodeOP_hash
 Cprotocols::jd3::JobGenealogist::JGResultNodeOP_hash
 Ccore::optimization::JJH_Minimizer
 Cprotocols::jd3::JobDigraphUpdaterThis class defines the set of operations that a JobQueen can perform to update the JobDigraph that she originally gave to the JobDistributor. In particular, the JobQueen may only update the JobDigraph by adding new nodes to the graph (which will receive incrementally larger indexes) and then adding edges to the graph such that the head node for the edge must land on one of the newly added nodes in the graph. The JobDistributor will hand the JobQueen a JobDigraphUpdater through the JobQueen's update_job_digraph method, and in this call, the JobQueen may add as many nodes as she wishes, and as many edges that land on those new nodes, but when the method exits, those nodes petrify: the JobQueen may not add any more edges that land on those new nodes
 Cprotocols::jd2::JobDistributor
 Cprotocols::jd3::JobDistributorFactory
 Cprotocols::jd2::JobDistributorFactory
 Cprotocols::jd2::JobOutputterObserver
 Cprotocols::multistage_rosetta_scripts::JobResultID_hash
 Cprotocols::jd3::JQKeyThis key can be used by to delineate other classes to store/maintain data used by the JQ
 Cprotocols::loops::JSONFormattedLoopsFileReader
 Ccore::kinematics::JumpObject which makes rigid-body transformation with translational and rotational perturbation
 Cprotocols::stepwise::modeler::rna::Jump_point
 Cprotocols::jumping::JumpSetup::JumpDef
 Cprotocols::jumping::ResiduePairJumpSetup::JumpDef
 Cprotocols::environment::claims::JumpElement
 Ccore::id::JumpID
 Cprotocols::jumping::JumpSample
 Cprotocols::jumping::JumpSelector::JumpWeightDef
 Ccore::pack::annealer::Key
 Ccore::pack::annealer::KeyHasher
 Ccore::scoring::fiber_diffraction::KromerMann
 Ccore::scoring::electron_density::KromerMann
 Cprotocols::kinmatch::KRSQuery
 Cprotocols::frag_picker::LAMBEGO_IO
 Ccore::optimization::lbfgs_iteration_data
 Cprotocols::loophash::LeapIndexStore information about a particular Leap
 Ccore::scoring::packstat::LeeRichards
 Cprotocols::loophash::LegacyLeapIndex
 Ccore::environment::LengthChecker
 Cprotocols::simple_moves::less_then_match_rmsd
 Ccore::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >Forward declaration for core::fragment::picking_old::concepts::Librarian
 Ccore::fragment::picking_old::concepts::Librarian< core::fragment::picking_old::vall::scores::VallFragmentScore, core::fragment::picking_old::vall::eval::VallFragmentEval, core::fragment::picking_old::vall::gen::VallFragmentGen, core::fragment::picking_old::vall::VallLibrary >
 Ccore::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >
 Ccore::fragment::picking_old::concepts::Library< Books >Forward declaration for Library
 Ccore::fragment::picking_old::concepts::Library< core::fragment::picking_old::vall::VallSections >
 Ccore::fragment::picking_old::concepts::Library< VallSections >
 Cprotocols::ligand_docking::Ligand_info
 Cprotocols::ligand_docking::ga_ligand_dock::LigandAlignerAligns ligand using defined constraint information
 Cprotocols::sewing::data_storage::LigandContact
 Cprotocols::sewing::hashing::LigandCoordInfo
 Cprotocols::sewing::data_storage::LigandDescription
 Ccore::sequence::LineStruct
 Cprotocols::forge::remodel::LineObject
 Ccore::chemical::carbohydrates::LinkageConformerDataHolds conformer data for glycan torsional sampling used by the LinkageConformerMover
 Ccore::io::LinkInformation
 Ccore::scoring::lkball::lkbtrie::LKBAtom
 Ccore::scoring::lkball::lkbtrie::LKBTrieEvaluator
 Ccore::scoring::hbonds::graph::LKHBondInfo
 Cprotocols::nmr::pcs::PCSLigandTransformMover::LMMinPCSDataRefUtility class of PCSLigandTransformMover which holds references to PCSData used in lmmin (Levenberg Marquardt minimization) function
 Cprotocols::loop_grower::LoopComparator
 Cprotocols::loops::LoopFromFileData
 Cprotocols::loophash::LoopHashMapLoop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates
 Cprotocols::denovo_design::task_operations::LoopInfo
 Cprotocols::loop_grower::LoopPartialSolution
 Cprotocols::loop_grower::LoopPartialSolutionStore
 CLowMemEdge
 CLowMemGraph
 CLowMemNode
 Ccore::scoring::packstat::LR_AtomData
 Ccore::scoring::packstat::LR_MP_AtomData
 Cstd::map< K, T >STL class
 Cprotocols::constraint_generator::AtomPairConstraintGenerator::MappedAtom
 Cprotocols::constel::MasterFilter
 Cprotocols::match::match_dspos1Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position)
 Cprotocols::match::match_lite_equals
 Cprotocols::match::match_lite_hasher
 Cprotocols::match::MatcherOutputStats
 Cprotocols::match::MatchOutputTracker
 Cprotocols::fldsgn::MatchResidues
 Cprotocols::cartesian::MD_Angle
 Cprotocols::cartesian::MD_Bond
 Cprotocols::cartesian::MD_HarmonicDihedral
 Cprotocols::md::MDscheduleData
 Cprotocols::mean_field::MeanFieldFactory
 Cprotocols::kinematic_closure::ClosureProblem::MementoSave the current state of the closure problem. This is meant to facilitate undoing rejected perturbations when necessary
 Ccore::chemical::MergeBehaviorManager
 Cprotocols::residue_optimization::MetapatchEnumeration
 Cprotocols::mpi_refinement::MethodParams
 Cprotocols::noesy_assign::MethylNames
 Cprotocols::features::MetricData
 Ccore::simple_metrics::MetricKeyThe key needed to set data in our SimpleMetricData. This allows only SimpleMetrics to set data
 Cprotocols::pose_metric_calculators::MetricValueGetter
 Ccore::optimization::symmetry::MinDebug
 Ccore::optimization::MinimizerSimple low-level minimizer class
 Cprotocols::frag_picker::quota::missing_fraction_sorter_biggest_first
 Ccore::chemical::MMAtomTypeBasic MM atom type
 Ccore::scoring::mm::MMBondAngleResidueTypeParam
 Ccore::select::movemap::MoveMapFactory::MMJumpActionAn action for a set of Jumps
 Ccore::select::movemap::MoveMapFactory::MMResActionAn action to be applied to a residue all members of a particular part (i.e. all backbone torsions, or all chi torsions)
 Ccore::select::movemap::MoveMapFactory::MMResIndexActionAn action for a particular indexed thing (i.e. a particular backbone, or a particular chi torsion)
 Cprotocols::legacy_sewing::ModelConstIterator< T >
 Cprotocols::legacy_sewing::ModelIterator< T >
 Ccore::io::ModifiedResidueInformation
 Cprotocols::cartesian::MolecularDynamics
 Ccore::chemical::sdf::MolWriter
 Cprotocols::motif_grafting::movers::motif2scaffold_dataStructure that contains the motif2scaffold_indexes data in a vector and adds fields for fragment matching information
 Cprotocols::motif_grafting::movers::motif2scaffold_indexesStructure that contains the data of corresponding fragments in the motif and scaffold
 Ccore::scoring::motif::MotifHit
 Cprotocols::motif_grafting::movers::MotifMatch
 Cprotocols::multistage_rosetta_scripts::mover_or_filter
 Cprotocols::wum::MoverList
 Cprotocols::jd2::MpiFileBuffer
 Cprotocols::canonical_sampling::MultiTemperatureTrialCounterKeep track of trial statistics for any number of replicas
 Ccore::chemical::MutableChiRecordA class containing bundled info about chis
 Ccore::chemical::MutableICoorRecordA basic class containing basic info of internal coordinates needed for building an atom within a ResidueType This is a simplified representation, used for MutableResidueType. It contains all the information, but is intended to be somewhat easier to update for added/deleted atoms than the standard AtomICoor
 Ccore::chemical::MutableResidueConnectionA simple class marking atoms at inter-residue connections
 Cprotocols::pmut_scan::Mutant
 Cprotocols::antibody::design::MutantPosition
 Cprotocols::pmut_scan::MutationData
 Cprotocols::simple_filters::SecretionPredictionFilter::mutt
 Cprotocols::fldsgn::MyAtom
 Ccore::scoring::motif::MyHash
 Ccore::scoring::motif::MyPred
 Ccore::pack::guidance_scoreterms::sap::MyTemplatePointerHash1< Tval >
 Ccore::pack::guidance_scoreterms::sap::MyTemplatePointerHash1< conformation::Residue >
 Ccore::id::NamedAtomIDAtom identifier class
 Ccore::id::NamedAtomID_Map< T >Map from Atom identifiers to contained values class
 Ccore::id::NamedAtomID_Map< NamedAtomID >
 Ccore::id::NamedStubID
 Cprotocols::constel::NeighTeller
 Ccore::optimization::NelderMeadSimplex
 Cprotocols::network::NetworkQueue
 Cprotocols::hbnet::NetworkState
 Cprotocols::hbnet::NetworkStateScoreComparator
 Cprotocols::simple_filters::nmer_svm_res_data
 Ccore::scoring::nmr::NMRGridSearch
 Ccore::pose::PDBPoseMap::no_segID_comp
 CNode
 Ccore::kinematics::Node
 Ccore::pack::interaction_graph::NodeBase
 Cprotocols::jd3::dag_node_managers::NodeManagerStorageMatrix
 Cnoncopyable
 Cprotocols::normalmode::NormalMode
 Ccore::pack::interaction_graph::NPDHBond
 Cprotocols::fold_from_loops::utils::NubSegment
 Cnull_bfs_prune_visitor
 Ccore::scoring::packstat::Octree2D
 Ccore::scoring::carbohydrates::OmegaPreferenceSamplingDataStruct for Omega-Preference dihedral sampling
 Ccore::scoring::fiber_diffraction::OneGaussianScattering
 Ccore::scoring::electron_density::OneGaussianScattering
 Cprotocols::toolbox::OP_const_iterator< const_iterator, SomeOP >Const_iterator class for SilentFileData container
 Cprotocols::optimize_weights::OptEPositionDataFactory
 Ccore::chemical::OrbitalBasic chemical atom
 Ccore::scoring::orbitals::OrbitalsStatistics
 Ccore::chemical::orbitals::OrbitalType
 Ccore::conformation::orbitals::OrbitalXYZCoords
 Ccore::scoring::packstat::OrderCavBallOnR
 Ccore::scoring::packstat::OrderCavBallOnRmAnb
 Ccore::scoring::packstat::OrderCavBallOnRmE
 Ccore::scoring::packstat::OrderCavBallOnX
 Ccore::scoring::packstat::OrderCBC
 Cprotocols::abinitio::OrderSortPredicate
 Ccore::scoring::packstat::OrderSphereOnID
 Ccore::scoring::packstat::OrderSphereOnX
 Cprotocols::constel::OrientCommonA class to hold data structures and functions common to filters that consider how groups of atoms within a constellation are oriented
 Cprotocols::stepwise::modeler::rna::output_data_struct
 Cprotocols::ligand_docking::ga_ligand_dock::OutputStructureStoreHelper class to manage multiple outputs
 Cprotocols::pose_creation::MergePDBMover::Overlap
 Cpair
 Ccore::scoring::custom_pair_distance::PairFuncMap
 Ccore::scoring::dssp::Pairing
 Cprotocols::abinitio::PairingStatEntry
 Cprotocols::jumping::PairingTemplate
 Cprotocols::indexed_structure_store::search::PairQueryExecutor
 Cprotocols::indexed_structure_store::search::PairQuerySummaryStatistics
 Ccore::io::nmr::ParaIon
 Ccore::conformation::parametric::ParameterizationCalculatorProperties
 Cprotocols::relax::CentroidRelax::parametersContainer for ramp settings
 Cprotocols::antibody::ParatopeMetric< T >Convenience struct for passing around paratope data, including individual data for cdrs. CDRs not present default to 0. Templates are used mainly to have core::Size/ Real or string values
 Cprotocols::antibody::ParatopeMetric< core::SSize >
 Cprotocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStepRepresents a step in the ParsedProtocol Note that one or more of mover/filter/metrics may be null/empty
 Cprotocols::multistage_rosetta_scripts::ParsedTagCache
 Ccore::id::PartialAtomIDPartial atom identifier class. Defined by an atom index and a residue number, or by an inter-residue-connection index, the number of bonds away from the inter-residue-connection atom, and a residue number
 Cprotocols::canonical_sampling::PatchOperation
 Cprotocols::pockets::PCluster@ Cluster of Pocket points
 Cprotocols::pockets::PClusterSet@ Set of cluster of pocket points
 Cprotocols::scoring::methods::pcs::PCS_data_inputPCS_data_input contain all the input information for the PCS. This includes all the information from the .npc files
 Cprotocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1
 Cprotocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2
 Cprotocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3
 Cprotocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
 Cprotocols::scoring::methods::pcsTs1::PCS_data_input_Ts1PCS_data_input_Ts1 contain all the input information for the PCS. This includes all the information from the .npc files
 Cprotocols::scoring::methods::pcsTs2::PCS_data_input_Ts2PCS_data_input_Ts2 contain all the input information for the PCS. This includes all the information from the .npc files
 Cprotocols::scoring::methods::pcsTs3::PCS_data_input_Ts3PCS_data_input_Ts3 contain all the input information for the PCS. This includes all the information from the .npc files
 Cprotocols::scoring::methods::pcsTs4::PCS_data_input_Ts4PCS_data_input_Ts4 contain all the input information for the PCS. This includes all the information from the .npc files
 Cprotocols::scoring::methods::pcs::PCS_data_per_lanthanides
 Cprotocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1
 Cprotocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2
 Cprotocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3
 Cprotocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
 Cprotocols::scoring::methods::pcs::PCS_file_dataPCS_file_data contain all the information of a .npc file one per lanthanide
 Cprotocols::scoring::methods::pcsTs1::PCS_file_data_Ts1PCS_file_data_Ts1 contain all the information of a .npc file one per lanthanide
 Cprotocols::scoring::methods::pcsTs2::PCS_file_data_Ts2PCS_file_data_Ts2 contain all the information of a .npc file one per lanthanide
 Cprotocols::scoring::methods::pcsTs3::PCS_file_data_Ts3PCS_file_data_Ts3 contain all the information of a .npc file one per lanthanide
 Cprotocols::scoring::methods::pcsTs4::PCS_file_data_Ts4PCS_file_data_Ts4 contain all the information of a .npc file one per lanthanide
 Cprotocols::scoring::methods::pcs::PCS_line_dataPCS_line_data class: hold a line of the input file information (.npc format) One PCS_line_data per line in the input file
 Cprotocols::scoring::methods::pcsTs1::PCS_line_data_Ts1PCS_line_data_Ts1 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts1 per line in the input file
 Cprotocols::scoring::methods::pcsTs2::PCS_line_data_Ts2PCS_line_data_Ts2 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts2 per line in the input file
 Cprotocols::scoring::methods::pcsTs3::PCS_line_data_Ts3PCS_line_data_Ts3 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts3 per line in the input file
 Cprotocols::scoring::methods::pcsTs4::PCS_line_data_Ts4PCS_line_data_Ts4 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts4 per line in the input file
 Cprotocols::scoring::methods::pcs::PCS_tensor
 Cprotocols::scoring::methods::pcsTs1::PCS_tensor_Ts1
 Cprotocols::scoring::methods::pcsTs2::PCS_tensor_Ts2
 Cprotocols::scoring::methods::pcsTs3::PCS_tensor_Ts3
 Cprotocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
 Cprotocols::scoring::methods::pcs2::PcsDataLanthanide
 Cprotocols::scoring::methods::pcs2::PcsEnergyParameter
 Cprotocols::scoring::methods::pcs2::PcsGridSearchParameter
 Cprotocols::scoring::methods::pcs2::PcsInputFilePcsInputFile contain all the information of a .npc file one per lanthanide
 Cprotocols::scoring::methods::pcs2::PcsInputLinePcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file
 Ccore::scoring::nmr::pcs::PCSMultiSet
 Ccore::scoring::nmr::pcs::PCSSingle
 Ccore::scoring::nmr::pcs::PCSSingleSet
 Cprotocols::scoring::methods::pcs2::PcsTensor
 Cprotocols::sparta::PDB
 Cprotocols::sparta::PDB_Entry
 Cprotocols::antibody::design::PDBNumberingSuper-basic numbering struct
 Cprotocols::noesy_assign::PeakAssignmentParameters
 Cprotocols::peptide_deriver::PeptideDeriverOutputterAbstract base class for handling calculation outputs from PeptideDeriverFilter Since PeptideDeriverFilter might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. This is an attempt to decouple the calculation from the representation of results. Representation of results is delegated to implementors of this class
 Cprotocols::analysis::PerResidueInterfaceDataAll per residue interface data and residue averages. Interface Residues only
 Cprotocols::ligand_docking::ga_ligand_dock::PharmacophorePharmacophore (aka binding-motif) definition
 Ccore::scoring::cryst::PhenixInterface
 Cprotocols::frag_picker::PhiPsiTalosIO
 Cprotocols::ligand_docking::ga_ligand_dock::PlaceableRotamer
 Ccore::scoring::packstat::Point
 Ccore::scoring::atomic_depth::point3d
 Ccore::pack::annealer::PointDwell
 Ccore::conformation::PointGraphEdgeData
 Ccore::conformation::PointGraphVertexData
 Cprotocols::pmut_scan::PointMutScanDriver
 Ccore::scoring::packstat::PointPair
 Cprotocols::electron_density::PointScoreComparator
 Ccore::chemical::PolarHydrogenFilterThe filter responsible for all polar hydrogens
 Cprotocols::nonlocal::PolicyFactory
 Cprotocols::sasa_scores::Poly
 CPolynomial_1d
 Cprotocols::canonical_sampling::mc_convergence_checks::PoolData
 Ccore::scoring::electron_density::poseCoord
 Cprotocols::multistage_rosetta_scripts::PoseForPoseIDWe do not want to load all of the input poses into memory at once. Instead we use this struct to keep track of the most recent pose loaded (which is assumed to be the most likely one we are going to need next)
 Ccore::io::pose_from_sfr::PoseFromSFRBuilderThe PoseFromSFRBuilder is responsible for taking a partially-processed representation of a structure file, a structure-file repersentation or StructFileRep, and it constructs a Pose from it. Its primary output is a Pose, but it also keeps track of the "missing atoms:" the set of atoms in the Pose whose coordinates were not given in the original file
 Cprotocols::loops::PoseNumberedLoopFileReader
 Cprotocols::indexed_structure_store::PoseUtilityPlaceholder
 Cprotocols::dna::PositionTypeBasic struct for remembering position/type information before/during/after design
 Ccore::scoring::power_diagram::PowerDiagram
 Cprotocols::sasa_scores::PPoly
 Ccore::init::pre_talaris_2013_behavior_settings
 Cprotocols::jd3::standard::PreliminaryLarvalJobA PreliminaryLarvalJob is what gets created from the command-line options job_definition file for each input and specified job in the Job Definition file
 Cprotocols::cluster::calibur::PreloadedPDB
 Ccore::scoring::nmr::pre::PREMultiSet
 Ccore::select::PreSelectedResidRange
 Cprotocols::constel::PresenceCommonA class to hold data structures and functions shared by filters that check whether the amino acids and atoms they require in the constellation are indeed present
 Ccore::scoring::nmr::pre::PRESingle
 Ccore::scoring::nmr::pre::PRESingleSet
 Ccore::pose::rna::principal_angle_degrees
 Ccore::pack::dunbrack::ProbSortClass
 Ccore::scoring::ProQPotential
 Cprotocols::ligand_docking::ProtLigPair_info
 Ccore::io::external::PsiPredResult
 Ccore::scoring::methods::PyEnergyMethodRegistratorThis class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
 Cprotocols::qsar::qsarOptData
 Cprotocols::simple_filters::Quat
 Cprotocols::frag_picker::quota::quota_limits_sorter_biggest_first
 Cprotocols::frag_picker::quota::quota_limits_sorter_smallest_first
 Cprotocols::frag_picker::quota::QuotaConfigRead a config file for quota selector
 Cprotocols::md::Rattle
 Ccore::io::raw_data::RawFileDataAbstract base class for classes that writes different types of silent-files that contain a mixture of Struct objects which are expected to be uniquely identified by some sort of string-based tag
 Cprotocols::pockets::ray_distance_derivs
 Cprotocols::electron_density::RBfitResult
 Cprotocols::electron_density::RBfitResultComparitor
 Cprotocols::rbsegment_relax::RBResidueRangeRB residue range
 Cprotocols::rbsegment_relax::RBSegmentRigid-body segments in a protein
 Ccore::scoring::RDC
 Ccore::scoring::RDC_Rohl
 Ccore::scoring::nmr::rdc::RDCMultiSet
 Ccore::scoring::nmr::rdc::RDCSingle
 Ccore::scoring::nmr::rdc::RDCSingleSet
 Ccore::chemical::rdkit::RDMolToRestype
 Ccore::chemical::RealFilterA filtered graph that doesn't contain fake/virtual atoms and fake/virtual bonds
 Ccore::chemical::RefConvert< OutRef >An internal implementation class, to get around the fact that functions cannot be partially specialized
 Ccore::chemical::RefConvert< core::Size >
 Ccore::chemical::RefConvert< std::string >
 Ccore::chemical::RefConvert< VD >
 Cprotocols::electron_density::RefinementResult
 Cprotocols::electron_density::RefinementResultComparitor
 Cprotocols::simple_filters::RegionalConnections
 Cprotocols::relax::RelaxScriptCommand
 Cprotocols::denovo_design::movers::RelaxScriptCommand
 Ccore::io::RemarkInfo
 Cprotocols::forge::remodel::RemodelData
 Cprotocols::forge::remodel::RemodelWorkingSet
 Cprotocols::protein_interface_design::ReportPSSMDifferences
 Cprotocols::protein_interface_design::ReportSequenceDifferences
 Ccore::chemical::RerootEdgeSorterEdge sorting: Return true if we should prefer edge1 over edge2
 Ccore::scoring::custom_pair_distance::resatom_and_func_struct
 Ccore::chemical::ResConnIDThe ResConnID could more properly be called the ResidueConnector. It stores the data necessary to describe how one ResidueConnection on a conformation::Residue is connected to the rest of the structure (Pose), by listing the other Residue's index and the ResidueConnection index
 Cprotocols::moves::ResId
 Cprotocols::stepwise::modeler::rna::Residue_info
 Ccore::scoring::annealing::ResidueArrayAnnealableEnergy
 Ccore::scoring::methods::ResidueAtomOverlaps
 Cprotocols::indexed_structure_store::ResidueBackboneEntry
 Cprotocols::abinitio::abscript::ResidueChunkSelection
 Ccore::chemical::ResidueConnectionA simple class marking atoms at inter-residue connections
 Cprotocols::simple_filters::ResidueDepthCalculator
 Cprotocols::simple_filters::ResidueDepthData
 Cprotocols::environment::claims::ResidueElement
 Cprotocols::indexed_structure_store::ResidueEntry
 Ccore::conformation::ResidueFactoryCollection of functions making a single residue
 Cprotocols::comparative_modeling::features::ResidueFeatureFactory
 Ccore::io::ResidueInformation
 Ccore::pose::PDBPoseMap::ResidueKeySortable residue key internal to PDBPoseMap
 Cprotocols::match::output::ResidueKinemageWriter
 Ccore::pack::task::ResidueLevelTask
 Cprotocols::indexed_structure_store::ResidueOrientEntry
 Ccore::select::residue_selector::ResidueRangeClass for storing a range of resids
 Ccore::pose::PDBInfo::ResidueRecordInternal struct for storing PDB residue related information
 Cprotocols::indexed_structure_store::ResidueSidechainEntry
 Cprotocols::toolbox::match_enzdes_util::ResInteractions
 Cprotocols::constel::ResMutA class to represent the mutation of a residue
 Ccore::io::raw_data::DisulfideFile::ResNumResidue of either pdb or rosetta numbering
 CResourceLoader
 CResourceLoaderCreator
 Ccore::scoring::motif::ResPairMotif
 Ccore::scoring::motif::ResPairMotifMetaBinner
 Ccore::scoring::motif::ResPairMotifQuery
 Cprotocols::loop_grower::ResTorsions
 Ccore::chemical::RestypeDestructionEventSpecial signal that the ResidueType is getting destroyed
 Cprotocols::dna::ResTypeSequence_lt
 Ccore::chemical::rdkit::RestypeToRDMol
 Cprotocols::electron_density::ResultDB< T, Tcomp >
 Cprotocols::jd3::dag_node_managers::ResultElements
 Cprotocols::dna::Reversion
 Cprotocols::protein_interface_design::Revert
 Cprotocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergyRotamer data used for packing in GALigandDock
 Ccore::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ReweightData
 Ccore::chemical::rings::RingConformerA structure for storing information for specific, idealized ring conformers
 Cprotocols::sparta::RingData
 Ccore::scoring::motif::RMSandEnergyCMP
 Cprotocols::loop_grower::RMSComparator
 Cprotocols::frags::RMSVallData
 Ccore::pose::rna::RNA_Datum
 Ccore::fragment::rna::RNA_FragmentHomologyExclusion
 Ccore::import_pose::RNA_HelixAssemblerThe RNA de novo structure modeling protocol
 Ccore::pose::rna::RNA_Reactivity
 Ccore::pose::rna::RNA_SuiteAssignment
 Ccore::pose::rna::RNA_SuiteInfo
 Ccore::chemical::carbohydrates::RootData
 Cprotocols::sic_dock::Rose
 CRosettaTensorflowProtocolBase
 Cprotocols::splice::ROT
 Ccore::scoring::trie::RotamerDescriptor< AT, CPDAT >
 Ccore::scoring::trie::RotamerDescriptorAtom< AT, CPDAT >
 Ccore::pack::interaction_graph::RotamerDotsCacheA lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes
 Cprotocols::features::RotamerInitializer< T, N >
 Cprotocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies
 Cprotocols::pose_metric_calculators::RotamerRecovery
 Ccore::pack::guidance_scoreterms::sap::RotamerRotamerHasher
 Cprotocols::ligand_docking::Rotate_info
 Cprotocols::denovo_design::movers::RotationRange
 Cprotocols::make_rot_lib::RotData
 Cprotocols::mean_field::RotProb
 Ccore::pack::annealer::RotSub
 Ccore::scoring::motif::RPM_FilterStats
 Ccore::kinematics::RTRotation + translation class
 Ccore::scoring::disulfides::RT_helper
 Ccore::pack::RTMin
 Cprotocols::make_rot_lib::running_average_pairStruct that is used in calc_centroids, values init to zero
 Cprotocols::match::upstream::SampleStrategyDataThis class holds all of the data associated with the logic for generating extra samples for a particular chi angle. There are tons of ways concievable to build extra rotamers; the data in this class is intended to group all of that data into one place. This class is not responsible for building extra rotamer samples; that responsibility is given to class FullChiSampleSet
 Cprotocols::features::strand_assembly::SandwichFragment
 Ccore::pack::guidance_scoreterms::sap::SapConstraintHelper
 Cprotocols::mpi_refinement::Scheduler
 Ccore::scoring::lkball::ScoredBridgingWater
 Cprotocols::electron_density::ScoredPoint
 Cprotocols::electron_density::ScoredPointCmptr
 Ccore::scoring::ScoreFunctionFactoryA collection of functions for making a single score_function
 Ccore::import_pose::atom_tree_diffs::ScoreLessThanComparatorProvides a StrictWeakOrdering comparator for sorting elements of a ScoresMap by one particular score type
 Ccore::scoring::ScoreTypeManager
 Ccore::sequence::ScoringSchemeFactory
 Ccore::kinematics::jacobian::ModuleType1::screw_construct_structStruct with the different linear algebra objects that are needed to express the twists and wrenches to calculate the instantaneous Jacobian matrices of the module
 Ccore::io::mmtf::sd_indexStorage for indicies to something in a mmtf struct this makes it easier to iterate the struct in relation to AtomInformation vectors
 Ccore::chemical::sdf::SDFParser
 Cprotocols::match::downstream::SecMatchEvaluatorFactoryCollection of functions making a single score_function
 Cprotocols::features::SecondaryStructureSegment
 Cprotocols::denovo_design::architects::SecStructInfo
 Cprotocols::features::Segment
 Cprotocols::legacy_sewing::segment
 Cprotocols::forge::remodel::Segment
 Cprotocols::denovo_design::components::SegmentCounts
 Cprotocols::indexed_structure_store::SegmentSequenceProfile
 Cprotocols::indexed_structure_store::SegmentSequenceProfileConfig
 Cprotocols::indexed_structure_store::SegmentSequenceProfileResult
 Cprotocols::seeded_abinitio::SegmentSpec
 Ccore::pack::annealer::SeqSymmAnnealerSetup
 Cprotocols::pose_metric_calculators::SequenceComparison
 Cprotocols::pdbinfo_manipulations::SequenceSpecificationRosetta defines the pdbinfo of an object via possible chain IDs, segment IDs, and insertion codes
 Cprotocols::mpi_refinement::Serial_Refine
 Cprotocols::loops::SerializedLoopBare-bones representation of a loop
 Cprotocols::network::NetworkQueue::ServerAddress
 Cstd::set< K >STL class
 Cprotocols::legacy_sewing::SewAtom
 Cprotocols::legacy_sewing::SewResidue
 Cprotocols::legacy_sewing::SewSegment
 Cprotocols::fldsgn::topology::SheetFoldTypeManager
 Ccore::io::SHEETInformation
 Cprotocols::loop_grower::SheetPositions
 Ccore::io::silent::SilentEnergyHelper class for silent-file classes to keep track of energy information
 Cprotocols::cluster::calibur::SimPDB
 CSimpleAssociates fragment indices with Gunn scores
 Ccore::simple_metrics::SimpleMetricStructStructure for all SimpleMetric Data. Used for mmTF IO and multistage protocols
 Ccore::scoring::packstat::SimplePDB
 Ccore::scoring::packstat::SimplePDB_Atom
 Ccore::scoring::epr_deer::Simulated4PDEERTrace
 Ccore::scoring::epr_deer::Simulated4PDEERTraceFactory
 Cprotocols::toolbox::match_enzdes_util::SingleConstraint
 Cprotocols::indexed_structure_store::search::SingleQueryExecutor
 Cprotocols::indexed_structure_store::search::SingleQuerySummaryStatistics
 Ccore::pack::dunbrack::SingleResidueDunbrackLibraryConcrete< T >
 Cprotocols::multistate_design::SingleStateEntityData
 CSingletonBase