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Class Hierarchy

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This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234567]
oCcore::scoring::sc::_ATOM_RADIUS
oCcore::scoring::sc::_DOT
oCprotocols::abinitio::_HashEntry
oCprotocols::abinitio::_MergableEntries
oCcore::scoring::sc::_PROBE
oCcore::scoring::sc::_RESULTS
oCA
oCA
oCA
oCAOf residues
oCA
oCcore::util::ABEGOAbego elments
oCprotocols::abinitio::AbrelaxApplicationApplication level code for Abrelax, Foldconstraints and JumpingFoldconstraints
oCutility::pointer::access_ptr
oCutility::pointer::access_ptr< Atom >
oCutility::pointer::access_ptr< AtomTree const >
oCutility::pointer::access_ptr< AtomTypeSet const >
oCutility::pointer::access_ptr< CentroidDisulfideEnergyContainer >
oCutility::pointer::access_ptr< CentroidDisulfideEnergyContainer const >
oCutility::pointer::access_ptr< CoarseEtable const >
oCutility::pointer::access_ptr< CrossPeak >
oCutility::pointer::access_ptr< DisulfideMatchingEnergyContainer >
oCutility::pointer::access_ptr< DisulfideMatchingEnergyContainer const >
oCutility::pointer::access_ptr< ElementSet const >
oCutility::pointer::access_ptr< EnzConstraintIO const >
oCutility::pointer::access_ptr< EnzConstraintParameters const >
oCutility::pointer::access_ptr< EnzdesFlexBBProtocol const >
oCutility::pointer::access_ptr< FlexbbRotamerSets const >
oCutility::pointer::access_ptr< FullatomDisulfideEnergyContainer >
oCutility::pointer::access_ptr< FullatomDisulfideEnergyContainer const >
oCutility::pointer::access_ptr< InvrotTreeNodeBase const >
oCutility::pointer::access_ptr< KinematicMover const >
oCutility::pointer::access_ptr< LoopMover_Refine_CCD >
oCutility::pointer::access_ptr< MetropolisHastingsMover >
oCutility::pointer::access_ptr< MMAtomTypeSet const >
oCutility::pointer::access_ptr< MMBondAngleLibrary const >
oCutility::pointer::access_ptr< OrbitalTypeSet const >
oCutility::pointer::access_ptr< Pose >
oCutility::pointer::access_ptr< Residue const >
oCutility::pointer::access_ptr< ResidueType const >
oCutility::pointer::access_ptr< ResidueTypeSet const >
oCutility::pointer::access_ptr< RNA_RawBaseBaseInfo >
oCutility::pointer::access_ptr< SecondaryMatchProtocol const >
oCutility::pointer::access_ptr< SingleResidueRotamerLibrary const >
oCutility::pointer::access_ptr< TopologyBroker const >
oCutility::pointer::access_ptr< VallProvider >
oCutility::pointer::access_ptr< WrapperOptEMultifunc >
oCcore::conformation::AddEdgeVisitor< Vertex, Edge >
oCcore::chemical::sdf::addedH
oCcore::chemical::AdductDescription of optional single-atom residue adducts
oCcore::sequence::AlignerFactory
oCprotocols::id::AlignmentIDUnique template identifier class
oCprotocols::comparative_modeling::AlignmentSet
oCAlternating
oCprotocols::abinitio::AlternativePairings
oCcore::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
oCcore::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >
oCAn
oCAn
oCprotocols::swa::rna::Anchor_ribose_stub
oCprotocols::sparta::ANN
oCcore::pack::annealer::AnnealerFactory
oCprotocols::antibody::AntibodyAntibody definition
oCprotocols::jd2::archive::ArchiveManagerArchiveManager 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
oCprotocols::mpi::ArchiveMasterBase
oCcore::graph::Array0< T >Class Array0 is a c-style array wrapper that does bounds checking in debug mode. It indexes from 0 just like regular c-arrays. Class Array0 does not manage it's own memory. It does not allocate memory if you want to make it larger, nor does it deallocate memory when you destroy it. Bounds checking only ensures that the user does not go outside of the memory Array0 thinks it's in charge of. If the user should happen to point the array0 at memory that has not been allocated, Array0 is not responsible for segmentation fault that will likely occur. Garbage in, garbage out
oCcore::graph::Array0< Real >
oCcore::scoring::packstat::Array2D
oCcore::graph::ArrayPoolElement< T >
oCcore::graph::ArrayPoolElement< Real >
oCcore::chemical::orbitals::AssignOrbitals
oCcore::chemical::AtomBasic chemical atom
oCcore::conformation::AtomA simple object with atom's position and its chemical type
oCprotocols::swa::rna::Atom_Bin
oCcore::chemical::AtomICoorA basic class containing info of internal coordinates needed for building an atom within a ResidueType
oCcore::id::AtomIDAtom identifier class. Defined by the atom number and the residue number
oCcore::id::AtomID_Map< T >Map from Atom identifiers to contained values class
oCcore::id::AtomID_Map< bool >
oCcore::id::AtomID_Map< core::id::AtomID >
oCcore::id::AtomID_Map< core::id::core::id::AtomID >
oCcore::id::AtomID_Map< core::Real >
oCcore::id::AtomID_Map< core::scoring::packstat::LR_AtomData >
oCcore::id::AtomID_Map< core::scoring::packstat::LR_MP_AtomData >
oCcore::id::AtomID_Map< core::Size >
oCcore::id::AtomID_Map< numeric::xyzVector< core::Real > >
oCcore::id::AtomID_Map< Size >
oCcore::id::AtomID_Map< tree::AtomOP >
oCcore::id::AtomID_Map< utility::vector1< Size > >
oCcore::io::pdb::AtomInformationA class that contains information for individual atoms
oCcore::scoring::AtomNeighborAtom-atom neighborlist object
oCcore::optimization::AtomNode
oCcore::scoring::etable::AtomPairEnergy
oCcore::scoring::packstat::AtomRadiusMap
oCcore::pose::PDBInfo::AtomRecordInternal struct for storing PDB atom related information
oCcore::scoring::custom_pair_distance::atoms_and_func_struct
oCcore::chemical::AtomTypeBasic atom type
oCcore::chemical::sdf::atomTyper
oCcore::kinematics::AtomWithDOFChangeSimple class for use in output-sensitive refold subroutine
oCprotocols::loophash::BackboneDB
oCprotocols::loophash::BackboneSegment
oCcore::pack::interaction_graph::BackgroundNode< V, E, G >A node which is not changing type or rotamer throughout a simulation
oCcore::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >An edge between a background node and a first class node
oCprotocols::backrub::BackrubSegmentClass for holind information about individual backrub segments
oCprotocols::swa::rna::Base_bin
oCcore::scoring::rna::Base_pair
oCcore::scoring::rna::Base_stack
oCprotocols::rna::BasePairType
oCstd::basic_string< Char >STL class
oCprotocols::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
oCcore::scoring::BB_Pos
oCprotocols::fldsgn::topology::BB_Pos
oCprotocols::loophash::BBData
oCcore::pack::dunbrack::BBDepNRChiSample< P >P for precision
oCcore::pack::dunbrack::BBDepNRChiSample< Real >
oCcore::pack::dunbrack::BBDepScoreInterpData
oCprotocols::loophash::BBExtraData
oCcore::pack::dunbrack::BBIndNRChiSample< P >
oCprotocols::forge::components::BDRSegmentInfo
oCcore::coarse::Rule::BeadAdder
oCcore::coarse::Translator::BeadAtom
oCbinary_function
oCBinaryExpression
oCprotocols::boinc::Boinc
oCprotocols::boinc::BoincSharedMemory
oCcore::chemical::sdf::BondData
oCcore::id::BondIDTwo more classes, temporary for testing purposes
oCcore::fragment::picking_old::concepts::Book< Pages >Forward declaration for Book
oCcore::fragment::picking_old::concepts::Book< core::fragment::picking_old::vall::VallResidues >
oCcore::fragment::picking_old::concepts::Book< VallResidues >
oCcore::fragment::picking_old::concepts::Bookmark< PageConstIterator >Forward declaration for core::fragment::picking_old::concepts::Bookmark
oCprotocols::match::Bool3DGridKinemageWriter
oCprotocols::branch_angle::BranchAngleOptimizer
oCprotocols::branch_angle::BranchCoef1Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors
oCprotocols::branch_angle::BranchParam1Class to store bond angle energy parameters around a single atom atom with three bonded neighbors
oCcore::io::serialization::BUFFER
oCcore::pack::rotamer_set::BumpSelector
oCprotocols::loophash::LoopHashMap::by_indexA functor for sort()
oCCacheableData
oCcore::pose::datacache::CacheableDataType
oCcore::pose::datacache::CacheableObserverType
oCcore::fragment::CacheWrapper< T, XCacheUnit >
oCcore::fragment::CacheWrapper< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::GunnTuple > >
oCcore::fragment::CacheWrapper< T, MapCacheUnit< T > >
oCcore::fragment::CacheWrapper< T, VectorCacheUnit< T > >
oCcore::pose::metrics::CalculatorFactory
oCprotocols::nonlocal::SmoothPolicy::Candidate
oCprotocols::cartesian::CartesianAtom
oCcore::scoring::packstat::CavityBall
oCcore::scoring::packstat::CavityBallCluster
oCprotocols::sic_dock::CBScoreVisitor
oCcore::scoring::disulfides::CentroidDisulfideEnergyComponentsStorage for Disulfide Energy Terms
oCcore::util::ChainbreakUtil
oCcore::pack::task::operation::ResiduePDBIndexIs::ChainPos
oCprotocols::qsar::scoring_grid::ChargeAtomVery light representation of an atom that is just a charge and a cartesian space position
oCcore::chemical::ChemicalManagerClass managing different sets of atom_type_set and residue_type_set
oCcore::scoring::packstat::Circle
oCprotocols::topology_broker::ClaimerMessage
oCprotocols::cluster::Cluster
oCprotocols::swa::rna::Cluster_Member
oCprotocols::toolbox::ClusterBase
oCprotocols::toolbox::ClusterOptions
oCprotocols::topology_broker::CmdLineData
oCprotocols::qsar::ColorGradient
oCprotocols::swa::rna::Combine_Tags_Info
oCprotocols::swa::rna::compare_base_bin
oCprotocols::swa::rna::compare_int_pair
oCprotocols::swa::rna::compare_test
oCprotocols::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
oCComputes
oCcore::conformation::signals::ConnectionEventSignal a change in the connection with a Conformation object, e.g. destruction or transfer
oCcore::io::raw_data::RawFileData::const_iteratorConst_iterator class for RawFileData container
oCcore::io::silent::SilentFileData::const_iteratorConst_iterator class for SilentFileData container
oCcore::scoring::constraints::ConstraintFactory
oCcore::scoring::constraints::ConstraintIO
oCprotocols::contact_map::ContactSimple class representing a contact between two atoms
oCprotocols::contact_map::ContactPartnerSimple class that holds the information on an atom involved in a contact
oCcore::scoring::ContextGraphFactory
oCcore::optimization::ConvergenceTest
oCprotocols::sparta::CORdata
oCprotocols::sic_dock::CorrectionVisitor
oCcore::scoring::etable::etrie::CountPairData_1_1
oCcore::scoring::etable::etrie::CountPairData_1_2
oCcore::scoring::etable::etrie::CountPairData_1_3
oCcore::scoring::etable::etrie::CountPairDataGeneric
oCcore::scoring::etable::count_pair::CountPairFactory
oCprotocols::noesy_assign::CovalentCompliance
oCcore::scoring::trie::CPDataCorrespondence
oCCrossoverBehavior
oCprotocols::frag_picker::CS2ndShift
oCcore::scoring::CSA
oCcore::chemical::CSDAtomTypeBasic "conformational" atom type derived from analysis of Cambridge Structure Database
oCprotocols::frag_picker::CSTalosIO
oCcore::chemical::sdf::CtabBase
oCcore::chemical::sdf::ctabV2000Parser
oCcore::chemical::sdf::ctabV3000Parser
oCprotocols::pockets::PCluster::Cxyz
oCcore::scoring::data_struct
oCcore::scoring::data_structDa
oCcore::scoring::data_structDaR
oCcore::scoring::data_structR
oCprotocols::canonical_sampling::mc_convergence_checks::DataBuffer
oCDataCache
oCprotocols::jd2::parser::DataLoaderFactoryA factory for creating DataLoaders, which are able to load arbitrary data into the DataMap used in the XML-based parser. This factory supports the load-time registration scheme allowing DataLoaders to be defined in libraries outside of protocols.lib
oCprotocols::cluster::DataPointData structure for one input data point for affinity propagation clustering
oCcore::scoring::DC
oCprotocols::ddG::ddGData
oCprotocols::hybridization::DDomainParse
oCcore::optimization::DerivCheckDataPoint
oCcore::scoring::DerivVectorPairA glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms
oCcore::optimization::DescentDirectionAlgorithm
oCcore::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
oCcore::pose::signals::DestructionEventSpecial signal that the Pose is getting destroyed
oCcore::graph::DisjointSets
oCprotocols::noesy_assign::FragsToAtomDist::DistanceRecord
oCprotocols::ligand_docking::DistributionMapA singleton class that returns a map of strings to enum types
oCcore::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
oCcore::io::raw_data::DisulfideFileParses and stores a disulfide file
oCcore::scoring::disulfides::DisulfideMatchingDatabase
oCcore::scoring::disulfides::DisulfideMatchingEnergyComponentsStorage for Disulfide Energy Terms
oCprotocols::jumping::DisulfPairing
oCprotocols::jumping::DisulfTemplate
oCprotocols::dna::DNABase
oCprotocols::dna::DNABasepair
oCprotocols::dna::DNABasestep
oCprotocols::dna::DnaNeighbor
oCprotocols::dna::DnaPosition
oCcore::optimization::DOF_DataPoint
oCcore::id::DOF_IDKinematics DOF identifier class
oCcore::id::DOF_ID_Map< T >Map from Atom DOF identifiers to contained values class
oCcore::id::DOF_ID_Map< utility::pointer::owning_ptr >
oCcore::id::DOF_ID_RangeKinematics DOF identifier (with range) class
oCprotocols::simple_moves::DOFHistogramRecorder
oCcore::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
oCprotocols::match::downstream_hit
oCcore::graph::DS_Node
oCcore::scoring::dssp::Dssp
oCcore::pack::dunbrack::DunbrackRotamerMeanSD< S, P >Forward declaration; default precision is DunbrackReal
oCcore::pack::dunbrack::DunbrackRotamerMeanSD< S, Real >
oCcore::pack::dunbrack::DunbrackRotamerSampleData
oCcore::graph::Edge
oCcore::kinematics::EdgeSingle edge of the fold_tree
oCcore::pack::interaction_graph::EdgeBase
oCcore::graph::EdgeListCustom edge list class. Returns const-iterators which only return Edge const *'s and non-const-iterators which can return either const or non-const Edge*'s. Manages its own memory using an unordered-object-pool for fast insertion and deletion of EdgeListElements. Implemented as a doubly linked list, though there's no practical way to start at the end of a list and work backward since decrementing the end iterator is not a valid operation
oCcore::graph::EdgeListConstIteratorCustom Edge list const iterator class, which returns only const Edge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL's const-iterator cannot be prevented from giving non-const access to its data. The former workaround to this problem was to define two sets of edge lists on each vertex: a list< Edge * > and a list< Edge const * >
oCcore::graph::EdgeListElementAn extensible graph class
oCcore::graph::EdgeListIteratorCustom Edge list (non-const) iterator class, which can return non-const Edge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL's const-iterator cannot be prevented from giving non-const access to its data. The former workaround to this problem was to define two sets of edge lists on each vertex: a list< Edge * > and a list< Edge const * >
oCcore::optimization::EItemInner class for Genetic Algorithm, hold one population with some additional info
oCcore::scoring::electron_density_atomwise::ElectronDensityAtomwise
oCcore::chemical::ElementClass to describe Elements
oCcore::chemical::sdf::elementToType
oCcore::scoring::EMapVectorA vector for storing energy data, initially all values are 0
oCprotocols::toolbox::pose_metric_calculators::EmptyVertexData
oCprotocols::wum2::EndPoint
oCprotocols::toolbox::pose_metric_calculators::EnergiesData
oCprotocols::genetic_algorithm::EntityElementsEqual
oCprotocols::pack_daemon::EntityHistoryLT
oCEntry
oCcore::scoring::etable::EtableEvaluator
oCcore::scoring::etable::EtableOptions
oCcore::scoring::etable::EtableParamsOnePair
oCprotocols::swa::rna::Euler_angles
oCprotocols::evaluation::EvaluatorFactoryCreate Evaluator Reporters
oCcore::scoring::packstat::Event
oCEXCN_BadInput
oCEXCN_Msg_Exception
oCprotocols::cluster::ExemplarData structure for one similarity measurement (s_ik) for affinity propagation clustering
oCcore::pack::interaction_graph::exposed_hydrophobic_data
oCExpression
oCExpressionCreator
oCcore::fragment::picking_old::concepts::Extent< PageIterator >Forward declaration for Extent
oCcore::fragment::picking_old::concepts::ExtentEvaluator< Bookmark, Ext >Forward declaration for core::fragments::picking_old::concepts::ExtentEvaluator
oCcore::fragment::picking_old::concepts::ExtentGenerator< Extent >Forward declaration for core::fragment::picking_old::concepts::ExtentGenerator
oCcore::scoring::etable::ExtraQuadraticRepulsion
oCFallbackConfiguration
oCFallbackConfigurationCreator
oCprotocols::protein_interface_design::FavorNativeResidue
oCprotocols::protein_interface_design::FavorNonNativeResidue
oCprotocols::swa::rna::FB_Pose_Data
oCprotocols::features::FeaturesReporterFactoryCreate Features Reporters
oCprotocols::checkpoint::FileBuffer
oCcore::io::pdb::FileDataFileData class. Hold data created from PDB file
oCprotocols::loophash::FilterBucket
oCprotocols::swa::rna::Filterer_Count
oCprotocols::filters::FilterFactory
oCprotocols::wum::find_SilentStructOPsThis little class is a predicate for finding silent structures in say a vector of silent structures
oCprotocols::flexpack::interaction_graph::FlexbbIGFactory
oCprotocols::flexpep_docking::FlexPepDockingPoseMetrics
oCprotocols::pockets::NonPlaidFingerprint::float4
oCprotocols::swa::rna::FloatingBaseChainClosureJobParameter
oCprotocols::noesy_assign::FoldResonance
oCcore::scoring::saxs::FormFactorManagerSelects a given number of fragments using a quota scheme
oCcore::fragment::FragFactory
oCcore::fragment::FragID
oCcore::fragment::FragmentIO
oCcore::fragment::picking_old::FragmentLibraryManagerSingleton class for accessing fragment libraries
oCprotocols::features::helixAssembly::FragmentPair
oCprotocols::antibody2::FrameWork
oCcore::scoring::disulfides::FullatomDisulfideEnergyComponents
oCcore::optimization::func_1d
oCcore::scoring::constraints::FuncFactory
oCG
oCcore::optimization::GA_Minimizer
oCcore::scoring::rna::Gaussian_parameter
oCprotocols::sparta::GDB
oCcore::pose::signals::GeneralEventSignals a general change in a Pose
oCcore::conformation::signals::GeneralEventSignals a general change in a Conformation
oCcore::scoring::etable::etrie::GenericResidueConnectionData
oCprotocols::viewer::GraphicsState
oCprotocols::qsar::scoring_grid::GridFactory
oCcore::scoring::geometric_solvation::GridInfo
oCprotocols::qsar::scoring_grid::GridManager
oCprotocols::scoring::methods::pcs2::GridSearchIteratorCA
oCprotocols::frag_picker::scores::GunnCost
oCprotocols::frag_picker::scores::GunnTuple
oCcore::scoring::Hairpin
oCcore::scoring::Hairpins
oCprotocols::match::downstream::hash_upstream_hit
oCcore::scoring::hbonds::hbtrie::HBAtom
oCcore::scoring::hbonds::hbtrie::HBCPData
oCcore::scoring::hbonds::HBEvalTuple
oCcore::scoring::hbonds::HBondDerivs
oCcore::scoring::hbonds::HBondTypeManager
oCcore::scoring::Helices
oCcore::pack::interaction_graph::history_queue_structFor storing three peices of associated data describing the recent history structure on a LinearMemNode
oCprotocols::match::Hit
oCcore::scoring::packing::HolesParams
oCcore::scoring::packing::HolesParamsRes
oCcore::scoring::packstat::HTL_EventX
oCprotocols::hybridization::HybridizeFoldtreeDynamic
oCcore::chemical::ICoorAtomIDAtom 's ID in internal coordinates in a ResidueType
oCcore::chemical::orbitals::ICoorOrbitalData
oCImplements
oCImplements
oCprotocols::inputter::Inputter
oCprotocols::inputter::InputterStream
oCprotocols::forge::remodel::RemodelMover::instruction_flags
oCcore::pack::interaction_graph::InteractionGraphFactory
oCprotocols::toolbox::InteratomicVarianceMatrix
oCprotocols::ligand_docking::ligand_options::InterfaceInfoInfo for each residue- is it part of the interface and if so, what ligands is it near
oCprotocols::swa::rna::InternalWorkingResidueParameter
oCprotocols::forge::build::IntervalSimple struct defining a closed interval of residues [left, right] where left <= right
oCprotocols::jumping::IntervalTwo numbers, i.e., jump start end residue, or cut-regions..
oCcore::scoring::etable::count_pair::Invoker
oCstd::ios_baseSTL class
oCprotocols::motifs::IRCollection
oCprotocols::simple_moves::LoggedFragmentMover::Item
oCprotocols::optimize_weights::IterativeOptEDriver
oCiterator
oCcore::io::raw_data::RawFileData::iteratorIterator class for RawFileData container
oCcore::io::silent::SilentFileData::iteratorIterator class for SilentFileData container
oCprotocols::frag_picker::JCouplingIO
oCcore::optimization::JJH_Minimizer
oCprotocols::jd2::JobDistributor
oCprotocols::jd2::JobDistributorFactory
oCprotocols::jd2::JobInputterFactory
oCprotocols::jd2::JobOutputterFactory
oCprotocols::loops::JSONFormattedLoopsFileReader
oCcore::kinematics::JumpObject which makes rigid-body transformation with translational and rotational perturbation
oCprotocols::swa::rna::Jump_point
oCprotocols::jumping::JumpSetup::JumpDef
oCprotocols::jumping::ResiduePairJumpSetup::JumpDef
oCcore::id::JumpID
oCprotocols::jumping::JumpSample
oCprotocols::jumping::JumpSelector::JumpWeightDef
oCcore::scoring::electron_density::KromerMann
oCprotocols::kinmatch::KRSQuery
oCprotocols::frag_picker::LAMBEGO_IO
oCLazyResourceManager
oCcore::optimization::lbfgs_iteration_data
oCprotocols::loophash::LeapIndexThe LeapIndex stores information about a particular Leap. It hold the oroiginal high precision rigid body transform and an Index to a Backbone Database (BackboneDB) that has the actual phi psi angles. THe storage of the precise RT takes a lot of space and may be deprecated at some point, since once it is hashed, it is rarely needed and can be recomputed if it is. Note that the length of the loop is not stored either, this is again done for saving memory, as huge lists of Leaps are typically created all with the same length. THe length is stored and handled by the owner of LeapIndex list. The LeapIndex does not store the actual backbone coordinates of the Leap. It merely contains an index (the BackboneIndex) which refers to a serial store of backbone triples (phi,psi, omega) which are stored somewhere else in a BackboneDB. THis is improtant to save memory storage since multiple Leaps cna share the same backbone triple and redundant storage would be hugely wasteful
oCcore::scoring::packstat::LeeRichards
oCprotocols::loophash::LegacyLeapIndex
oCcore::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >Forward declaration for core::fragment::picking_old::concepts::Librarian
oCcore::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 >
oCcore::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >
oCcore::fragment::picking_old::concepts::Library< Books >Forward declaration for Library
oCcore::fragment::picking_old::concepts::Library< core::fragment::picking_old::vall::VallSections >
oCcore::fragment::picking_old::concepts::Library< VallSections >
oCprotocols::ligand_docking::Ligand_info
oCcore::util::LineStruct
oCprotocols::forge::remodel::LineObject
oCcore::io::pdb::LinkInformationA structure for storing information from PDB LINK records
oCprotocols::loops::LoopFromFileData
oCprotocols::loophash::LoopHashMapLoop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates
oCprotocols::loops::LoopMoverFactoryCreate LoopMover Reporters
oCprotocols::loops::loop_mover::refine::LoopRefineInnerCycleFactoryCreate LoopMover Reporters
oCprotocols::loops::loops_definers::LoopsDefinerFactoryCreate LoopsDefiner Reporters
oCcore::scoring::packstat::LR_AtomData
oCcore::scoring::packstat::LR_MP_AtomData
oCprotocols::match::match_dspos1Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position)
oCprotocols::match::match_lite_equals
oCprotocols::match::match_lite_hasher
oCprotocols::match::MatcherOutputStats
oCprotocols::match::MatchOutputTracker
oCprotocols::fldsgn::MatchResidues
oCprotocols::cartesian::MD_Angle
oCprotocols::cartesian::MD_Bond
oCprotocols::cartesian::MD_HarmonicDihedral
oCprotocols::noesy_assign::MethylNameLibrary
oCprotocols::noesy_assign::MethylNames
oCprotocols::toolbox::pose_metric_calculators::MetricValueGetter
oCcore::optimization::symmetry::MinDebug
oCcore::optimization::MinimizerSimple low-level minimizer class
oCprotocols::frag_picker::quota::missing_fraction_sorter_biggest_first
oCcore::chemical::MMAtomTypeBasic MM atom type
oCcore::scoring::mm::MMBondAngleResidueTypeParam
oCcore::chemical::sdf::MolData
oCprotocols::cartesian::MolecularDynamics
oCcore::scoring::sc::MolecularSurfaceCalculator
oCcore::chemical::sdf::MolFileParser
oCcore::chemical::sdf::MolWriter
oCprotocols::moves::MoverFactory
oCprotocols::wum::MoverList
oCprotocols::jd2::MpiFileBuffer
oCprotocols::canonical_sampling::MultiTemperatureTrialCounter
oCprotocols::pmut_scan::Mutant
oCprotocols::pmut_scan::MutationData
oCprotocols::fldsgn::MyAtom
oCcore::id::NamedAtomIDAtom identifier class
oCcore::id::NamedStubID
oCcore::graph::NegSpaceElement< T >NegSpaceElement represents a single element in the singly-linked list of negative space in an array pool
oCcore::graph::NegSpaceElement< Real >
oCcore::graph::Node
oCcore::kinematics::Node
oCcore::pack::interaction_graph::NodeBase
oCnoncopyable
oCcore::scoring::packstat::Octree2D
oCcore::scoring::electron_density::OneGaussianScattering
oCprotocols::toolbox::OP_const_iterator< const_iterator, SomeOP >Const_iterator class for SilentFileData container
oCprotocols::optimize_weights::OptEPositionDataFactory
oCcore::chemical::OrbitalBasic chemical atom
oCcore::scoring::orbitals::OrbitalsAssigned
oCcore::scoring::orbitals::OrbitalsStatistics
oCcore::chemical::orbitals::OrbitalType
oCcore::chemical::orbitals::OrbitalTypeMapper
oCcore::conformation::orbitals::OrbitalXYZCoords
oCcore::scoring::packstat::OrderCavBallOnR
oCcore::scoring::packstat::OrderCavBallOnRmAnb
oCcore::scoring::packstat::OrderCavBallOnRmE
oCcore::scoring::packstat::OrderCavBallOnX
oCcore::scoring::packstat::OrderCBC
oCcore::scoring::packstat::OrderSphereOnID
oCcore::scoring::packstat::OrderSphereOnX
oCprotocols::swa::rna::output_data_struct
oCprotocols::rotamer_recovery::RRReporterSQLite::OutputLevel
oCprotocols::outputter::Outputter
oCutility::pointer::owning_ptr
oCutility::pointer::owning_ptr< Ab_TemplateInfo >
oCutility::pointer::owning_ptr< ABEGO_SS_Map >
oCutility::pointer::owning_ptr< AbinitioMoverWeight >
oCutility::pointer::owning_ptr< AbstractArchiveBase >
oCutility::pointer::owning_ptr< Accumulator >
oCutility::pointer::owning_ptr< ActiveSiteGrid >
oCutility::pointer::owning_ptr< ActiveSiteGrid const >
oCutility::pointer::owning_ptr< AlignPoseToInvrotTreeMover >
oCutility::pointer::owning_ptr< AllowedSeqposForGeomCst >
oCutility::pointer::owning_ptr< AllowedSeqposForGeomCst const >
oCutility::pointer::owning_ptr< AllowInsert >
oCutility::pointer::owning_ptr< Anchor const >
oCutility::pointer::owning_ptr< AnchorMoversData >
oCutility::pointer::owning_ptr< AntibodyInfo >
oCutility::pointer::owning_ptr< APBSConfig >
oCutility::pointer::owning_ptr< APBSResult >
oCutility::pointer::owning_ptr< ArchiveBase >
oCutility::pointer::owning_ptr< AtomPairFuncList const >
oCutility::pointer::owning_ptr< AtomTree >
oCutility::pointer::owning_ptr< AtomTreeCollection >
oCutility::pointer::owning_ptr< AtomTreeMinimizer >
oCutility::pointer::owning_ptr< BackrubMover >
oCutility::pointer::owning_ptr< BaseJumpSetup >
oCutility::pointer::owning_ptr< BasicJob const >
oCutility::pointer::owning_ptr< BatchFeatures >
oCutility::pointer::owning_ptr< BluePrint >
oCutility::pointer::owning_ptr< Bool3DGrid >
oCutility::pointer::owning_ptr< BoundedQuotaContainer >
oCutility::pointer::owning_ptr< BuildManager >
oCutility::pointer::owning_ptr< BumpGrid >
oCutility::pointer::owning_ptr< BumpGrid const >
oCutility::pointer::owning_ptr< CarbohydrateInfo >
oCutility::pointer::owning_ptr< CarbonHBondPotential >
oCutility::pointer::owning_ptr< CartBondedParameters const >
oCutility::pointer::owning_ptr< CB_Angle_Func >
oCutility::pointer::owning_ptr< CBSG_Dihedral_Func >
oCutility::pointer::owning_ptr< CDRsMinPackMin >
oCutility::pointer::owning_ptr< Cell >
oCutility::pointer::owning_ptr< CenHBPotential >
oCutility::pointer::owning_ptr< CentroidDisulfidePotential >
oCutility::pointer::owning_ptr< ChangeFoldTreeMover >
oCutility::pointer::owning_ptr< CheckPointer >
oCutility::pointer::owning_ptr< ClassicFragmentMover >
oCutility::pointer::owning_ptr< ClassicMatchAlgorithm const >
oCutility::pointer::owning_ptr< ClusterBase >
oCutility::pointer::owning_ptr< CoarseRNA_LoopCloser >
oCutility::pointer::owning_ptr< ConformerSwitchMover >
oCutility::pointer::owning_ptr< ConstantLengthFragSet >
oCutility::pointer::owning_ptr< Constraint const >
oCutility::pointer::owning_ptr< ConstraintClaimer const >
oCutility::pointer::owning_ptr< ConstraintEvaluator >
oCutility::pointer::owning_ptr< ConstraintGraph >
oCutility::pointer::owning_ptr< Constraints >
oCutility::pointer::owning_ptr< ConstraintSet >
oCutility::pointer::owning_ptr< ConstraintSet const >
oCutility::pointer::owning_ptr< ConstraintSetMover >
oCutility::pointer::owning_ptr< core::grid::CartGrid< int > >
oCutility::pointer::owning_ptr< core::scoring::constraints::AngleConstraint >
oCutility::pointer::owning_ptr< CrossPeakInfo >
oCutility::pointer::owning_ptr< CrossPeakInfo const >
oCutility::pointer::owning_ptr< CrossPeakList >
oCutility::pointer::owning_ptr< CycleMover >
oCutility::pointer::owning_ptr< DaemonSet >
oCutility::pointer::owning_ptr< DatabaseFilter >
oCutility::pointer::owning_ptr< DatabaseOccSolEne >
oCutility::pointer::owning_ptr< ddG >
oCutility::pointer::owning_ptr< DdgFilter >
oCutility::pointer::owning_ptr< DDPlookup >
oCutility::pointer::owning_ptr< DesignRepackMover >
oCutility::pointer::owning_ptr< DesignVsNativeComparison >
oCutility::pointer::owning_ptr< DirectReadoutPotential >
oCutility::pointer::owning_ptr< DistanceFunc const >
oCutility::pointer::owning_ptr< DisulfideMatchingPotential >
oCutility::pointer::owning_ptr< DNA_BasePotential >
oCutility::pointer::owning_ptr< DnaChains >
oCutility::pointer::owning_ptr< DnaInterfaceFinder >
oCutility::pointer::owning_ptr< DnaInterfacePacker >
oCutility::pointer::owning_ptr< DockingEnsemble >
oCutility::pointer::owning_ptr< DockingHighRes >
oCutility::pointer::owning_ptr< DockingHighResFilter >
oCutility::pointer::owning_ptr< DockingInitialPerturbation >
oCutility::pointer::owning_ptr< DockingLowRes >
oCutility::pointer::owning_ptr< DockingLowResFilter >
oCutility::pointer::owning_ptr< DockingProtocol >
oCutility::pointer::owning_ptr< DockMCMCycle >
oCutility::pointer::owning_ptr< DockMCMProtocol >
oCutility::pointer::owning_ptr< DockTaskFactory >
oCutility::pointer::owning_ptr< DOF_Node >
oCutility::pointer::owning_ptr< DofClaim >
oCutility::pointer::owning_ptr< DownstreamAlgorithm >
oCutility::pointer::owning_ptr< DownstreamBuilder >
oCutility::pointer::owning_ptr< DownstreamBuilder const >
oCutility::pointer::owning_ptr< DownstreamCoordinateKinemageWriter >
oCutility::pointer::owning_ptr< DownstreamCoordinateKinemageWriter const >
oCutility::pointer::owning_ptr< Energies >
oCutility::pointer::owning_ptr< EnergyGraph >
oCutility::pointer::owning_ptr< EnergyMethodOptions >
oCutility::pointer::owning_ptr< EntityCorrespondence >
oCutility::pointer::owning_ptr< EnvPairPotential >
oCutility::pointer::owning_ptr< EnzConstraintIO >
oCutility::pointer::owning_ptr< EnzConstraintIO const >
oCutility::pointer::owning_ptr< EnzCstTemplateRes >
oCutility::pointer::owning_ptr< EnzdesCstCache >
oCutility::pointer::owning_ptr< EnzdesLoopsFile >
oCutility::pointer::owning_ptr< EnzdesLoopsFile const >
oCutility::pointer::owning_ptr< EnzdesScorefileFilter >
oCutility::pointer::owning_ptr< EnzdesSeqRecoveryCache >
oCutility::pointer::owning_ptr< evaluation::SingleValuePoseEvaluator< T > const >
oCutility::pointer::owning_ptr< FaDockingSlideIntoContact >
oCutility::pointer::owning_ptr< FASTERInteractionGraph >
oCutility::pointer::owning_ptr< FastRelax >
oCutility::pointer::owning_ptr< Filter >
oCutility::pointer::owning_ptr< Filter const >
oCutility::pointer::owning_ptr< FilterCollection >
oCutility::pointer::owning_ptr< FilterStructs >
oCutility::pointer::owning_ptr< FlexbbInteractionGraph >
oCutility::pointer::owning_ptr< FlexbbRotamerSets const >
oCutility::pointer::owning_ptr< FlexPepDockingFlags const >
oCutility::pointer::owning_ptr< FoldTree >
oCutility::pointer::owning_ptr< FragData >
oCutility::pointer::owning_ptr< FragmentCost >
oCutility::pointer::owning_ptr< FragmentMover >
oCutility::pointer::owning_ptr< FragmentSampler >
oCutility::pointer::owning_ptr< FragmentScoreManager >
oCutility::pointer::owning_ptr< FragmentSelectingRule >
oCutility::pointer::owning_ptr< FragSet >
oCutility::pointer::owning_ptr< FragSet const >
oCutility::pointer::owning_ptr< FragsToAtomDist >
oCutility::pointer::owning_ptr< Frame >
oCutility::pointer::owning_ptr< FrameIteratorWorker_ >
oCutility::pointer::owning_ptr< FullatomDisulfidePotential >
oCutility::pointer::owning_ptr< Func >
oCutility::pointer::owning_ptr< GenBornPotential >
oCutility::pointer::owning_ptr< GenericMonteCarloMover >
oCutility::pointer::owning_ptr< genetic_algorithm::GeneticAlgorithm >
oCutility::pointer::owning_ptr< GeomSampleInfo >
oCutility::pointer::owning_ptr< Graph >
oCutility::pointer::owning_ptr< Graph const >
oCutility::pointer::owning_ptr< GreenPacker >
oCutility::pointer::owning_ptr< GroupDiscriminator >
oCutility::pointer::owning_ptr< GuardedLoopsFromFile >
oCutility::pointer::owning_ptr< H3CterInsert >
oCutility::pointer::owning_ptr< H3PerturbCCD >
oCutility::pointer::owning_ptr< HarmonicFunc >
oCutility::pointer::owning_ptr< HBondDatabase const >
oCutility::pointer::owning_ptr< HBondOptions >
oCutility::pointer::owning_ptr< HBondOptions const >
oCutility::pointer::owning_ptr< HBondResidueMinData const >
oCutility::pointer::owning_ptr< HeaderInformation >
oCutility::pointer::owning_ptr< HedgeArchive >
oCutility::pointer::owning_ptr< HelicalFragment >
oCutility::pointer::owning_ptr< HierarchicalLevel >
oCutility::pointer::owning_ptr< HotspotStubSet >
oCutility::pointer::owning_ptr< IdealParametersDatabase >
oCutility::pointer::owning_ptr< IGEdgeReweightContainer >
oCutility::pointer::owning_ptr< ImplicitFastClashCheck const >
oCutility::pointer::owning_ptr< IndependentLoopMover >
oCutility::pointer::owning_ptr< InnerJob >
oCutility::pointer::owning_ptr< InnerMultiThreadingJob >
oCutility::pointer::owning_ptr< InputStreamWithResidueInfo >
oCutility::pointer::owning_ptr< InteractionGraphBase >
oCutility::pointer::owning_ptr< Interface >
oCutility::pointer::owning_ptr< InterfaceAnalyzerMover >
oCutility::pointer::owning_ptr< InterfaceBuilder >
oCutility::pointer::owning_ptr< InterfaceSasaFilter >
oCutility::pointer::owning_ptr< InterfaceTaskOperation >
oCutility::pointer::owning_ptr< InvrotTree >
oCutility::pointer::owning_ptr< InvrotTree const >
oCutility::pointer::owning_ptr< IterativeVectorExpression >
oCutility::pointer::owning_ptr< Job >
oCutility::pointer::owning_ptr< JobDataFeatures >
oCutility::pointer::owning_ptr< JobInputter >
oCutility::pointer::owning_ptr< JobOutputter >
oCutility::pointer::owning_ptr< JumpCalculator >
oCutility::pointer::owning_ptr< KinematicControl >
oCutility::pointer::owning_ptr< KinematicMover >
oCutility::pointer::owning_ptr< KinematicPerturber >
oCutility::pointer::owning_ptr< LHRepulsiveRamp >
oCutility::pointer::owning_ptr< LHSnugFitLegacy >
oCutility::pointer::owning_ptr< LigandMotifSearch >
oCutility::pointer::owning_ptr< LocalInserter >
oCutility::pointer::owning_ptr< LocalInserter_SimpleMin >
oCutility::pointer::owning_ptr< LoopHashLibrary >
oCutility::pointer::owning_ptr< LoopHashSampler >
oCutility::pointer::owning_ptr< LoopRelaxMover >
oCutility::pointer::owning_ptr< Loops >
oCutility::pointer::owning_ptr< Loops const >
oCutility::pointer::owning_ptr< LoopsFileIO >
oCutility::pointer::owning_ptr< MatchConstraintFileInfo const >
oCutility::pointer::owning_ptr< Matcher const >
oCutility::pointer::owning_ptr< MatchEvaluator >
oCutility::pointer::owning_ptr< MatchGrouper >
oCutility::pointer::owning_ptr< MaxSeqSepConstraintSet >
oCutility::pointer::owning_ptr< Membrane_FAPotential >
oCutility::pointer::owning_ptr< MembraneJump >
oCutility::pointer::owning_ptr< MembranePotential >
oCutility::pointer::owning_ptr< MetaPoseEvaluator >
oCutility::pointer::owning_ptr< MetropolisHastingsMover >
oCutility::pointer::owning_ptr< MinimizationGraph >
oCutility::pointer::owning_ptr< MinimizerOptions >
oCutility::pointer::owning_ptr< MiniPose >
oCutility::pointer::owning_ptr< MinMover >
oCutility::pointer::owning_ptr< MMBondAngleLibrary >
oCutility::pointer::owning_ptr< MMBondAngleResidueTypeParamSet >
oCutility::pointer::owning_ptr< MMBondLengthLibrary >
oCutility::pointer::owning_ptr< MMLJEnergyTable >
oCutility::pointer::owning_ptr< MMLJLibrary >
oCutility::pointer::owning_ptr< MMTorsionLibrary >
oCutility::pointer::owning_ptr< MonteCarlo >
oCutility::pointer::owning_ptr< Motif const >
oCutility::pointer::owning_ptr< MotifSearch >
oCutility::pointer::owning_ptr< MoveMap >
oCutility::pointer::owning_ptr< MoveMap const >
oCutility::pointer::owning_ptr< MoveMapBuilder >
oCutility::pointer::owning_ptr< Mover >
oCutility::pointer::owning_ptr< MultipleDomainMover >
oCutility::pointer::owning_ptr< MultistateAggregateFunction >
oCutility::pointer::owning_ptr< MultiStateAggregateFunction const >
oCutility::pointer::owning_ptr< MultiStatePacker >
oCutility::pointer::owning_ptr< NeighborList >
oCutility::pointer::owning_ptr< NoesyModule >
oCutility::pointer::owning_ptr< numeric::interpolation::spline::Interpolator >
oCutility::pointer::owning_ptr< NumericalDerivCheckResult >
oCutility::pointer::owning_ptr< NVlookup >
oCutility::pointer::owning_ptr< NVscore >
oCutility::pointer::owning_ptr< OccupiedSpaceHash >
oCutility::pointer::owning_ptr< OccupiedSpaceHash const >
oCutility::pointer::owning_ptr< OmegaTether >
oCutility::pointer::owning_ptr< OptEData >
oCutility::pointer::owning_ptr< OptEMultifunc >
oCutility::pointer::owning_ptr< OrbitalsLookup >
oCutility::pointer::owning_ptr< OrderedFragSet >
oCutility::pointer::owning_ptr< OtherContextScoreFunction >
oCutility::pointer::owning_ptr< OutputWriter >
oCutility::pointer::owning_ptr< P_AA >
oCutility::pointer::owning_ptr< PackerTask >
oCutility::pointer::owning_ptr< PackerTask const >
oCutility::pointer::owning_ptr< PackRotamersMover >
oCutility::pointer::owning_ptr< PairEPotential >
oCutility::pointer::owning_ptr< PairingStatistics const >
oCutility::pointer::owning_ptr< Parser >
oCutility::pointer::owning_ptr< PBLifetimeCache >
oCutility::pointer::owning_ptr< PCA >
oCutility::pointer::owning_ptr< PdbDataFeatures >
oCutility::pointer::owning_ptr< PDBInfo >
oCutility::pointer::owning_ptr< PDBOutput >
oCutility::pointer::owning_ptr< PDBPoseMap const >
oCutility::pointer::owning_ptr< PDDFEnergy >
oCutility::pointer::owning_ptr< PeakAssignmentResidueMap >
oCutility::pointer::owning_ptr< PeptideStapleMover >
oCutility::pointer::owning_ptr< PlacementAuctionMover >
oCutility::pointer::owning_ptr< PlacementMinimizationMover >
oCutility::pointer::owning_ptr< PocketGrid >
oCutility::pointer::owning_ptr< PointGraph >
oCutility::pointer::owning_ptr< PoissonBoltzmannPotential >
oCutility::pointer::owning_ptr< Policy >
oCutility::pointer::owning_ptr< Pool_RMSD >
oCutility::pointer::owning_ptr< Pose >
oCutility::pointer::owning_ptr< Pose const >
oCutility::pointer::owning_ptr< PoseCommentsFeatures >
oCutility::pointer::owning_ptr< PoseCondition >
oCutility::pointer::owning_ptr< PoseConformationFeatures >
oCutility::pointer::owning_ptr< PoseFilter >
oCutility::pointer::owning_ptr< PoseInputStream >
oCutility::pointer::owning_ptr< PoseMetricContainer >
oCutility::pointer::owning_ptr< PosePackData >
oCutility::pointer::owning_ptr< PQR >
oCutility::pointer::owning_ptr< Predicate const >
oCutility::pointer::owning_ptr< ProteinResidueConformationFeatures >
oCutility::pointer::owning_ptr< ProteinSCSampler const >
oCutility::pointer::owning_ptr< ProteinSilentReport >
oCutility::pointer::owning_ptr< Protocol >
oCutility::pointer::owning_ptr< ProtocolFeatures >
oCutility::pointer::owning_ptr< protocols::cluster::ClusterPhilStyle >
oCutility::pointer::owning_ptr< protocols::moves::DataMapObj< std::string > >
oCutility::pointer::owning_ptr< protocols::moves::protocols::moves::DataMapObj< bool > >
oCutility::pointer::owning_ptr< protocols::moves::protocols::moves::DataMapObj< std::string > >
oCutility::pointer::owning_ptr< protocols::moves::protocols::moves::DataMapObj< utility::utility::vector1< core::Size > > >
oCutility::pointer::owning_ptr< protocols::moves::protocols::moves::DataMapObj< utility::vector1< core::Size > > >
oCutility::pointer::owning_ptr< qsarMap >
oCutility::pointer::owning_ptr< QuickRepacker >
oCutility::pointer::owning_ptr< QuotaCollector >
oCutility::pointer::owning_ptr< Ramachandran >
oCutility::pointer::owning_ptr< Ramachandran2B >
oCutility::pointer::owning_ptr< RandomMover >
oCutility::pointer::owning_ptr< RefineOneCDRLoop >
oCutility::pointer::owning_ptr< Region >
oCutility::pointer::owning_ptr< RelativeSequencePosition >
oCutility::pointer::owning_ptr< RelaxProtocolBase >
oCutility::pointer::owning_ptr< Remarks >
oCutility::pointer::owning_ptr< RemodelConstraintGenerator >
oCutility::pointer::owning_ptr< ResfileContents const >
oCutility::pointer::owning_ptr< ResFilter >
oCutility::pointer::owning_ptr< ResidualDipolarCoupling >
oCutility::pointer::owning_ptr< Residue >
oCutility::pointer::owning_ptr< Residue const >
oCutility::pointer::owning_ptr< ResidueConformationFeatures >
oCutility::pointer::owning_ptr< ResidueCoordinateChangeList >
oCutility::pointer::owning_ptr< ResidueFeatures >
oCutility::pointer::owning_ptr< ResiduePairJump >
oCutility::pointer::owning_ptr< ResiduePairJumpSetup >
oCutility::pointer::owning_ptr< ResidueType >
oCutility::pointer::owning_ptr< ResidueType const >
oCutility::pointer::owning_ptr< ResLvlTaskOperation >
oCutility::pointer::owning_ptr< ResolutionSwitcher >
oCutility::pointer::owning_ptr< ResonanceList >
oCutility::pointer::owning_ptr< RestrictConservedLowDdgOperation >
oCutility::pointer::owning_ptr< RestrictResidueToRepacking >
oCutility::pointer::owning_ptr< ReturnSidechainMover >
oCutility::pointer::owning_ptr< RigidBodyDofSeqPerturbMover >
oCutility::pointer::owning_ptr< RigidBodyInfo >
oCutility::pointer::owning_ptr< RigidBodyPerturbMover >
oCutility::pointer::owning_ptr< RigidBodyPerturbNoCenterMover >
oCutility::pointer::owning_ptr< RNA_AddMover >
oCutility::pointer::owning_ptr< RNA_AddOrDeleteMover >
oCutility::pointer::owning_ptr< RNA_AtomVDW >
oCutility::pointer::owning_ptr< RNA_CentroidInfo >
oCutility::pointer::owning_ptr< RNA_ChunkLibrary >
oCutility::pointer::owning_ptr< RNA_DataReader >
oCutility::pointer::owning_ptr< RNA_DeleteMover >
oCutility::pointer::owning_ptr< RNA_FragmentMover >
oCutility::pointer::owning_ptr< RNA_Fragments >
oCutility::pointer::owning_ptr< RNA_JumpLibrary >
oCutility::pointer::owning_ptr< RNA_LoopCloser >
oCutility::pointer::owning_ptr< RNA_LowResolutionPotential >
oCutility::pointer::owning_ptr< RNA_Mg_KnowledgeBasedPotential >
oCutility::pointer::owning_ptr< RNA_Minimizer >
oCutility::pointer::owning_ptr< RNA_O2StarMover >
oCutility::pointer::owning_ptr< RNA_Relaxer >
oCutility::pointer::owning_ptr< RNA_StructureParameters >
oCutility::pointer::owning_ptr< RNA_TorsionMover >
oCutility::pointer::owning_ptr< RNA_TorsionPotential >
oCutility::pointer::owning_ptr< RotamerBoltzmannWeight >
oCutility::pointer::owning_ptr< RotamerCouplings const >
oCutility::pointer::owning_ptr< RotamerLibraryScratchSpace >
oCutility::pointer::owning_ptr< RotamerLinks const >
oCutility::pointer::owning_ptr< RotamerOperation >
oCutility::pointer::owning_ptr< RotamerRecovery >
oCutility::pointer::owning_ptr< RotamerSet >
oCutility::pointer::owning_ptr< RotamerSet const >
oCutility::pointer::owning_ptr< RotamerSetOperation >
oCutility::pointer::owning_ptr< RotamerSets >
oCutility::pointer::owning_ptr< RotamerTrialsMinMover >
oCutility::pointer::owning_ptr< RotamerTrialsMover >
oCutility::pointer::owning_ptr< RRComparer >
oCutility::pointer::owning_ptr< RRProtocol >
oCutility::pointer::owning_ptr< RRReporter >
oCutility::pointer::owning_ptr< SameStrand >
oCutility::pointer::owning_ptr< SaneMinMover >
oCutility::pointer::owning_ptr< ScoreCutoffFilter >
oCutility::pointer::owning_ptr< ScoreFunction >
oCutility::pointer::owning_ptr< ScoreFunction const >
oCutility::pointer::owning_ptr< ScoreFunctionInfo >
oCutility::pointer::owning_ptr< ScoreTypeFeatures >
oCutility::pointer::owning_ptr< SearchPattern >
oCutility::pointer::owning_ptr< SecondaryStructure >
oCutility::pointer::owning_ptr< SecondaryStructure const >
oCutility::pointer::owning_ptr< SecondaryStructurePotential >
oCutility::pointer::owning_ptr< SelectRDC_Evaluator >
oCutility::pointer::owning_ptr< SelectResiduesByLayer >
oCutility::pointer::owning_ptr< SequenceAlignment >
oCutility::pointer::owning_ptr< SequenceAlignment const >
oCutility::pointer::owning_ptr< SequenceMapping const >
oCutility::pointer::owning_ptr< SequenceMover >
oCutility::pointer::owning_ptr< SequenceProfile >
oCutility::pointer::owning_ptr< SequenceProfile const >
oCutility::pointer::owning_ptr< SG_Dist_Func >
oCutility::pointer::owning_ptr< SGSG_Dihedral_Func >
oCutility::pointer::owning_ptr< ShearMover >
oCutility::pointer::owning_ptr< ShortestPathInFoldTree >
oCutility::pointer::owning_ptr< ShortRangeTwoBodyEnergy >
oCutility::pointer::owning_ptr< SidechainContactDistCutoff >
oCutility::pointer::owning_ptr< SidechainMinMover >
oCutility::pointer::owning_ptr< SidechainMover >
oCutility::pointer::owning_ptr< SilentFileData >
oCutility::pointer::owning_ptr< SilentFileJobOutputter >
oCutility::pointer::owning_ptr< SilentFilePoseInputStream >
oCutility::pointer::owning_ptr< SimpleInteractionGraph >
oCutility::pointer::owning_ptr< SingleGrid >
oCutility::pointer::owning_ptr< SingleStateFitnessFunction const >
oCutility::pointer::owning_ptr< SingleStructureData >
oCutility::pointer::owning_ptr< SlidingWindowLoopClosure >
oCutility::pointer::owning_ptr< SmallMover >
oCutility::pointer::owning_ptr< SmoothEnvPairPotential >
oCutility::pointer::owning_ptr< StepWiseJobParameters >
oCutility::pointer::owning_ptr< StepWisePoseSampleGenerator >
oCutility::pointer::owning_ptr< StepWisePoseSetup >
oCutility::pointer::owning_ptr< StepWiseRNA_BaseCentroidScreener >
oCutility::pointer::owning_ptr< StepWiseRNA_JobParameters >
oCutility::pointer::owning_ptr< StepWiseRNA_JobParameters const >
oCutility::pointer::owning_ptr< StepWiseRNA_VDW_Bin_Screener >
oCutility::pointer::owning_ptr< StrandPairing >
oCutility::pointer::owning_ptr< StrandPairingSet >
oCutility::pointer::owning_ptr< StructureFeatures >
oCutility::pointer::owning_ptr< StructureScoresFeatures >
oCutility::pointer::owning_ptr< StubScoreFilter >
oCutility::pointer::owning_ptr< SumFunc >
oCutility::pointer::owning_ptr< SurfaceParameters >
oCutility::pointer::owning_ptr< SwitchResidueTypeSetMover >
oCutility::pointer::owning_ptr< SymDockingHiRes >
oCutility::pointer::owning_ptr< SymDockingLowRes >
oCutility::pointer::owning_ptr< SymDockProtocol >
oCutility::pointer::owning_ptr< SymmData >
oCutility::pointer::owning_ptr< SymmetricRotamerSets >
oCutility::pointer::owning_ptr< SymmetricScoreFunction >
oCutility::pointer::owning_ptr< SymmetryInfo >
oCutility::pointer::owning_ptr< SymmetryInfo const >
oCutility::pointer::owning_ptr< SymMinMover >
oCutility::pointer::owning_ptr< SymPackRotamersMover >
oCutility::pointer::owning_ptr< SymRotamerTrialsMover >
oCutility::pointer::owning_ptr< TargetRotamerCoords >
oCutility::pointer::owning_ptr< TaskFactory >
oCutility::pointer::owning_ptr< TaskFactory const >
oCutility::pointer::owning_ptr< TaskOperation >
oCutility::pointer::owning_ptr< TCacheUnit >
oCutility::pointer::owning_ptr< TemperatureController >
oCutility::pointer::owning_ptr< TemperatureController const >
oCutility::pointer::owning_ptr< TemperingBase >
oCutility::pointer::owning_ptr< Templates >
oCutility::pointer::owning_ptr< Templates const >
oCutility::pointer::owning_ptr< ThermodynamicMover >
oCutility::pointer::owning_ptr< TopologyBroker >
oCutility::pointer::owning_ptr< TrialMover >
oCutility::pointer::owning_ptr< UnboundRotamersOperation >
oCutility::pointer::owning_ptr< UnfoldedStatePotential >
oCutility::pointer::owning_ptr< UpstreamCollisionFilter const >
oCutility::pointer::owning_ptr< UpstreamDownstreamCollisionFilter const >
oCutility::pointer::owning_ptr< UpstreamHitCacher >
oCutility::pointer::owning_ptr< UpstreamResTypeGeometry >
oCutility::pointer::owning_ptr< utility::in_place_list< int > >
oCutility::pointer::owning_ptr< VallChunk >
oCutility::pointer::owning_ptr< VallProvider >
oCutility::pointer::owning_ptr< VarianceStatisticsArchive >
oCutility::pointer::owning_ptr< VarLengthBuild >
oCutility::pointer::owning_ptr< VectorExpression const >
oCutility::pointer::owning_ptr< WaterAdductHBondPotential >
oCutility::pointer::owning_ptr< WrapperOptEMultifunc >
oCutility::pointer::owning_ptr< WriteUpstreamHitKinemage >
oCcore::scoring::dssp::Pairing
oCprotocols::abinitio::PairingStatEntry
oCprotocols::jumping::PairingTemplate
oCprotocols::relax::CentroidRelax::parametersContainer for ramp settings
oCprotocols::canonical_sampling::PatchOperation
oCprotocols::pockets::PCluster@
oCprotocols::pockets::PClusterSet@
oCprotocols::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
oCprotocols::scoring::methods::pcs::PCS_data_input_manager
oCprotocols::scoring::methods::pcs::PCS_data_per_lanthanides
oCprotocols::scoring::methods::pcs::PCS_Energy_parameters_manager
oCprotocols::scoring::methods::pcs::PCS_file_dataPCS_file_data contain all the information of a .npc file one per lanthanide
oCprotocols::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
oCprotocols::scoring::methods::pcs::PCS_tensor
oCprotocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
oCprotocols::scoring::methods::pcs2::PcsDataLanthanide
oCprotocols::scoring::methods::pcs2::PcsEnergyParameter
oCprotocols::scoring::methods::pcs2::PcsEnergyParameterManager
oCprotocols::scoring::methods::pcs2::PcsGridSearchParameter
oCprotocols::scoring::methods::pcs2::PcsGridSearchParameterManager
oCprotocols::scoring::methods::pcs2::PcsInputCenterManager
oCprotocols::scoring::methods::pcs2::PcsInputFilePcsInputFile contain all the information of a .npc file one per lanthanide
oCprotocols::scoring::methods::pcs2::PcsInputLinePcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file
oCprotocols::scoring::methods::pcs2::PcsTensor
oCprotocols::sparta::PDB
oCcore::io::pdb::PDB_DReaderPDB Reader it self, D - for dynamic approch of type handling
oCprotocols::noesy_assign::PeakAssignmentParameters
oCprotocols::frag_picker::PhiPsiTalosIO
oCcore::scoring::packstat::Point
oCcore::conformation::PointGraphEdgeData
oCcore::conformation::PointGraphVertexData
oCprotocols::pmut_scan::PointMutScanDriver
oCcore::scoring::packstat::PointPair
oCprotocols::nonlocal::PolicyFactory
oCprotocols::sasa_scores::Poly
oCPolynomial_1d
oCpool
oCprotocols::canonical_sampling::mc_convergence_checks::PoolData
oCprotocols::swa::rna::pose_data_struct2
oCprotocols::loops::PoseNumberedLoopFileReader
oCprotocols::dna::PositionTypeBasic struct for remembering position/type information before/during/after design
oCprotocols::sasa_scores::PPoly
oCcore::pack::dunbrack::ProbSortClass
oCcore::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
oCprotocols::qsar::qsarOptData
oCprotocols::simple_filters::Quat
oCprotocols::frag_picker::quota::quota_limits_sorter_biggest_first
oCprotocols::frag_picker::quota::quota_limits_sorter_smallest_first
oCprotocols::frag_picker::quota::QuotaConfigRead a config file for quota selector
oCcore::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
oCprotocols::pockets::ray_distance_derivs
oCprotocols::rbsegment_relax::RBResidueRangeRB residue range
oCprotocols::rbsegment_relax::RBSegmentRigid-body segments in a protein
oCcore::scoring::RDC
oCcore::scoring::RDC_Rohl
oCutility::pointer::ReferenceCount