| Ccore::scoring::sc::_ATOM_RADIUS | |
| Ccore::scoring::sc::_DOT | |
| Ccore::scoring::sc::_PROBE | |
| Ccore::scoring::sc::_RESULTS | |
| Ccore::util::ABEGO | Abego elments |
| Ccore::chemical::AcceptorAtomFilter | The filter responsible for obtaining all acceptor atoms |
| Ccore::conformation::AddEdgeVisitor< Vertex, Edge > | |
| Ccore::chemical::Adduct | Description of optional single-atom residue adducts |
| Ccore::sequence::AlignerFactory | |
| Ccore::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | |
| Ccore::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::float > | |
| Ccore::pack::annealer::AnnealerFactory | |
| Ccore::chemical::APolarHydrogenFilter | The filter responsible for all apolar hydrogens |
| Ccore::chemical::AromaticAtomFilter | The filter responsible for all aromatic atoms |
| Ccore::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 |
| Ccore::graph::Array0< double > | |
| Ccore::scoring::packstat::Array2D | |
| Ccore::graph::ArrayPoolElement< T > | |
| Ccore::graph::ArrayPoolElement< double > | |
| Ccore::chemical::orbitals::AssignOrbitals | |
| Ccore::chemical::Atom | |
| ►Ccore::conformation::Atom | |
| Ccore::scoring::elec::ElecAtom | |
| Ccore::scoring::etable::etrie::EtableAtom | |
| Ccore::scoring::mm::mmtrie::MMEnergyTableAtom | |
| Ccore::chemical::AtomICoor | A basic class containing info of internal coordinates needed for building an atom within a ResidueType |
| Ccore::id::AtomID | Atom 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_AtomID | |
| ►Ccore::id::AtomID_Map< bool > | |
| Ccore::id::AtomID_Map_bool | |
| Ccore::id::AtomID_Map< core::double > | |
| 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< double > | |
| Ccore::id::AtomID_Map< numeric::xyzVector< core::double > > | |
| ►Ccore::id::AtomID_Map< Real > | |
| Ccore::id::AtomID_Map_Real | |
| Ccore::id::AtomID_Map< Size > | |
| Ccore::id::AtomID_Map< tree::AtomOP > | |
| Ccore::id::AtomID_Map< utility::vector1< Size > > | |
| Ccore::io::pdb::AtomInformation | A class that contains information for individual atoms |
| Ccore::scoring::AtomNeighbor | Atom-atom neighborlist object |
| Ccore::optimization::AtomNode | |
| Ccore::scoring::etable::AtomPairEnergy | |
| Ccore::scoring::packstat::AtomRadiusMap | |
| Ccore::pose::PDBInfo::AtomRecord | Internal struct for storing PDB atom related information |
| Ccore::scoring::custom_pair_distance::atoms_and_func_struct | |
| Ccore::chemical::AtomType | Basic atom type |
| CAtomTypeData | Hybridization and bond geometry data, which is used in Atom |
| Ccore::kinematics::AtomWithDOFChange | Simple class for use in output-sensitive refold subroutine |
| ►Ccore::pack::interaction_graph::BackgroundNode< V, E, G > | A node which is not changing type or rotamer throughout a simulation |
| Ccore::pack::interaction_graph::HPatchBackgroundNode< V, E, G > | Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable |
| Ccore::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > | Defines a BackgroundResidue node which will contribute to changes in surface energy due to state changes on neighboring nodes, and not because of state changes to it |
| ►Ccore::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > | An edge between a background node and a first class node |
| Ccore::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > | Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) |
| Ccore::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > | Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) |
| Ccore::pose::rna::BasePair | |
| Ccore::pose::rna::BaseStack | |
| ►Cstd::basic_string< Char > | STL class |
| ►Cstd::string | STL class |
| Ccore::sequence::AnnotatedSequence | |
| Ccore::scoring::BB_Pos | |
| Ccore::pack::dunbrack::BBDepNRChiSample< P > | P for precision |
| Ccore::pack::dunbrack::BBDepNRChiSample< double > | |
| Ccore::pack::dunbrack::BBDepScoreInterpData | |
| Ccore::pack::dunbrack::BBIndNRChiSample< P > | |
| Ccore::coarse::Translator::BeadAtom | |
| Ccore::indexed_structure_store::BinaryFragmentStoreBackend | |
| Ccore::chemical::Bond | Basic chemical Bond |
| Ccore::chemical::sdf::BondData | |
| Ccore::id::BondID | Two more classes, temporary for testing purposes |
| 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 | |
| ►Ccore::fragment::picking_old::concepts::Book< VallResidues > | |
| Ccore::fragment::picking_old::vall::VallSection | Class implementing the Book concept for a continuous section of lines in the Vall library |
| Ccore::fragment::picking_old::concepts::Bookmark< PageConstIterator > | Forward declaration for core::fragment::picking_old::concepts::Bookmark |
| Ccore::io::serialization::BUFFER | |
| Ccore::pack::rotamer_set::BumpSelector | |
| ►Cbasic::datacache::CacheableData [external] | |
| Ccore::id::CacheableAtomID_MapVector | AtomID_Map< xyzVector< Real > > |
| Ccore::pack::rotamer_set::WaterPackingInfo | |
| Ccore::pose::datacache::CacheablePoseRawPtr | Pose * |
| Ccore::pose::datacache::PositionConservedResiduesStore | |
| Ccore::pose::full_model_info::FullModelInfo | Keep track of all information related to how a subpose 'fits in' to global modeling scheme |
| Ccore::scoring::CenListInfo | Keep track of the cenlist information |
| Ccore::scoring::ChemicalShiftAnisotropy | ChemicalShiftAnisotropys are mainly handled by this class |
| Ccore::scoring::constraints::CstMinimizationData | |
| Ccore::scoring::custom_pair_distance::RespairInteractions | |
| Ccore::scoring::DipolarCoupling | DipolarCouplings are mainly handled by this class |
| Ccore::scoring::disulfides::DisulfMinData | |
| Ccore::scoring::dna::BasePartner | Silly vector1 wrapper class so we can derive from PoseCachedData |
| Ccore::scoring::elec::FAElecContextData | |
| Ccore::scoring::FACTSPoseInfo | |
| Ccore::scoring::FACTSRotamerSetInfo | |
| Ccore::scoring::GenBornPoseInfo | |
| Ccore::scoring::GenBornRotamerSetInfo | |
| Ccore::scoring::hbonds::HBondResidueMinData | A class to hold data for the HBondEnergy class used in score and derivative evaluation |
| Ccore::scoring::hbonds::HBondResPairMinData | |
| Ccore::scoring::hbonds::HBondSet | A class that holds Hbond objects and helps setup Hbonds for scoring |
| Ccore::scoring::Membrane_FAEmbed | Membrane Fullatom embedding info |
| Ccore::scoring::MembraneEmbed | Whole Pose Membrane Embedding |
| Ccore::scoring::MembraneTopology | |
| Ccore::scoring::methods::LKB_ResidueInfo | |
| Ccore::scoring::methods::LKB_ResiduesInfo | |
| Ccore::scoring::methods::LKB_ResPairMinData | |
| Ccore::scoring::methods::PBLifetimeCache | |
| ►Ccore::scoring::methods::RG_MinData | |
| Ccore::scoring::methods::RG_Local_MinData | |
| Ccore::scoring::ResidualDipolarCoupling | ResidualDipolarCouplings are mainly handled by this class |
| Ccore::scoring::ResidualDipolarCoupling_Rohl | |
| Ccore::scoring::ResidueNblistData | |
| Ccore::scoring::ResiduePairNeighborList | |
| Ccore::scoring::rna::RNA_CentroidInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| Ccore::scoring::rna::RNA_FilteredBaseBaseInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| Ccore::scoring::rna::RNA_RawBaseBaseInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! / Also, should probably use EnergyGraph instead of FArrays – much smaller memory footprint (!) / |
| Ccore::scoring::rna::RNA_ScoringInfo | Keep track of RNA centroid, useful atom, base-base info inside the pose |
| Ccore::scoring::SigmoidWeightedCenList< T > | Keep track of the cenlist information stores both centroid counts (T = Real) as well as d_centroid_counts (T = Vector) |
| Ccore::scoring::SS_Info | |
| Ccore::scoring::SS_Killhairpins_Info | |
| Ccore::scoring::symmetry::NBListCache | |
| Ccore::scoring::trie::TrieCollection | |
| Ccore::sequence::CacheableSequenceProfile | |
| Ccore::pose::datacache::CacheableDataType | |
| Ccore::pose::datacache::CacheableObserverType | |
| Ccore::fragment::CacheWrapper< T, XCacheUnit > | |
| ►Ccore::fragment::CacheWrapper< T, MapCacheUnit< T > > | |
| Ccore::fragment::FragCache< T > | |
| ►Ccore::fragment::CacheWrapper< T, VectorCacheUnit< T > > | |
| Ccore::fragment::FragStore< T > | |
| Ccore::pose::metrics::CalculatorFactory | |
| Ccore::scoring::packstat::CavityBall | |
| Ccore::scoring::packstat::CavityBallCluster | |
| Ccore::scoring::disulfides::CentroidDisulfideEnergyComponents | Storage for Disulfide Energy Terms |
| Ccore::pack::dunbrack::cenrot::CentroidRotamerSampleData | Simple class storing all the data for one centroid-rotamer well |
| Ccore::util::ChainbreakUtil | |
| Ccore::pack::task::operation::ResiduePDBIndexIs::ChainPos | |
| Ccore::scoring::packstat::Circle | |
| Ccore::scoring::sc::CloserToAtom | A small struct to report which of two atoms is closer to a given atom: |
| CComputes | |
| Ccore::conformation::signals::ConnectionEvent | Signal a change in the connection with a Conformation object, e.g. destruction or transfer |
| Ccore::io::raw_data::RawFileData::const_iterator | Const_iterator class for RawFileData container |
| Ccore::io::silent::SilentFileData::const_iterator | Const_iterator class for SilentFileData container |
| Ccore::scoring::ContextGraphFactory | |
| ►Ccore::optimization::ConvergenceTest | |
| Ccore::optimization::DFPMinConvergedAbsolute | |
| Ccore::optimization::DFPMinConvergedFractional | |
| Ccore::chemical::CopyEdge< Graph1, Graph2 > | |
| Ccore::chemical::CopyVertex< Graph1, Graph2 > | |
| 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::trie::CPDataCorrespondence | |
| ►CCrossoverBehavior | |
| Ccore::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > | |
| Ccore::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > | |
| Ccore::pose::CrystInfo | |
| Ccore::scoring::CSA | |
| ►Ccore::chemical::sdf::CtabParserBase | |
| Ccore::chemical::sdf::CtabV2000Parser | |
| Ccore::chemical::sdf::CtabV3000Parser | |
| Ccore::scoring::etable::CubicPolynomial | |
| Ccore::scoring::data_struct | |
| Ccore::scoring::data_structDa | |
| Ccore::scoring::data_structDaR | |
| Ccore::scoring::data_structR | |
| ►Cbasic::datacache::DataCache< CacheableObserver > [external] | |
| Ccore::pose::datacache::ObserverCache | A DataCache storing Pose/Conformation observers derived from core::pose::datacache::CacheableObserver |
| ►Cbasic::datacache::DataCache< datacache::CacheableObserver > [external] | |
| Ccore::pose::Py_basic_datacache_DataCache_CacheableObserver | |
| Ccore::scoring::DC | |
| ►Cdefault_dfs_visitor | |
| Ccore::chemical::RerootRestypeVisitor | |
| Ccore::optimization::DerivCheckDataPoint | |
| Ccore::scoring::DerivVectorPair | A glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms |
| Ccore::optimization::DescentDirectionAlgorithm | |
| Ccore::io::sequence_comparation::DesignContrast | DesignContrast 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::DestructionEvent | Special signal that the Pose is getting destroyed |
| Ccore::graph::DisjointSets | |
| Ccore::scoring::disulfides::DisulfideAtomIndices | This 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::DisulfideFile | Parses and stores a disulfide file |
| Ccore::scoring::disulfides::DisulfideMatchingDatabase | |
| Ccore::scoring::disulfides::DisulfideMatchingEnergyComponents | Storage for Disulfide Energy Terms |
| Ccore::optimization::DOF_DataPoint | |
| Ccore::id::DOF_ID | Kinematics 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_Range | Kinematics DOF identifier (with range) class |
| Ccore::pack::interaction_graph::DotSphere | Represents the sphere of dots on the vdW surface of an atom, for use in the LeGrand and Merz method of calculating SASA |
| Ccore::graph::DS_Node | |
| Ccore::scoring::dssp::Dssp | |
| ►Ccore::pack::dunbrack::DunbrackRotamerMeanSD< S, P > | Forward declaration; default precision is DunbrackReal |
| Ccore::pack::dunbrack::DunbrackRotamer< S, P > | Forward declaration; default precision is DunbrackReal |
| Ccore::pack::dunbrack::PackedDunbrackRotamer< S, P > | Forward declaration; default precision is DunbrackReal; |
| ►Ccore::pack::dunbrack::DunbrackRotamerMeanSD< S, double > | |
| Ccore::pack::dunbrack::DunbrackRotamer< T, double > | |
| Ccore::pack::dunbrack::DunbrackRotamerSampleData | |
| ►Ccore::graph::Edge | |
| Ccore::pack::interaction_graph::SimpleEdge | |
| Ccore::scoring::constraints::ConstraintEdge | |
| Ccore::scoring::EnergyEdge | |
| Ccore::scoring::MinimizationEdge | |
| Ccore::scoring::TenANeighborEdge | |
| Ccore::scoring::TwelveANeighborEdge | |
| Ccore::kinematics::Edge | Single edge of the fold_tree |
| ►Ccore::pack::interaction_graph::EdgeBase | |
| ►Ccore::pack::interaction_graph::FixedBBEdge | |
| ►Ccore::pack::interaction_graph::OnTheFlyEdge | |
| Ccore::pack::interaction_graph::DoubleLazyEdge | |
| Ccore::pack::interaction_graph::LazyEdge | |
| Ccore::pack::interaction_graph::LinearMemEdge | |
| ►Ccore::pack::interaction_graph::PrecomputedPairEnergiesEdge | |
| Ccore::pack::interaction_graph::DensePDEdge | |
| Ccore::pack::interaction_graph::DoubleDensePDEdge | |
| Ccore::pack::interaction_graph::FASTEREdge | |
| Ccore::pack::interaction_graph::PDEdge | |
| ►Ccore::pack::interaction_graph::SymmOnTheFlyEdge | |
| Ccore::pack::interaction_graph::SymmLinearMemEdge | |
| Ccore::pack::interaction_graph::SymmMinimalistEdge | |
| Ccore::graph::EdgeList | Custom 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 |
| Ccore::graph::EdgeListConstIterator | Custom 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 * > |
| Ccore::graph::EdgeListElement | An extensible graph class |
| Ccore::graph::EdgeListIterator | Custom 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 * > |
| Ccore::optimization::EItem | Inner class for Genetic Algorithm, hold one population with some additional info |
| Ccore::scoring::elec::ElecGroup | |
| Ccore::chemical::ElectronConfiguration | Describes the electron configuration of atoms |
| Ccore::scoring::electron_density_atomwise::ElectronDensityAtomwise | |
| Ccore::scoring::EMapVector | A vector for storing energy data, initially all values are 0 |
| ►Cenable_shared_from_this | |
| Ccore::chemical::ResidueType | A class for defining a type of residue |
| Ccore::chemical::ResidueTypeSet | A collection of ResidueType defined |
| ►Ccore::conformation::Conformation | A container of Residues and the kinematics to manage them |
| Ccore::conformation::symmetry::SymmetricConformation | A symmetric conformation: has an additional data member "SymmetryInfo" class |
| Ccore::conformation::parametric::Parameters | Parameters class, used to store sets of parameters for parametric backbone generation |
| Ccore::conformation::parametric::ParametersSet | ParametersSet class, used to store sets of parameters for parametric backbone generation |
| Ccore::conformation::Residue | Instance Residue class, used for placed residues and rotamers |
| ►Ccore::fragment::FragData | |
| Ccore::fragment::AnnotatedFragData | FragData that contains additional information |
| ►Ccore::graph::Graph | A Graph with constant time edge insertion and deletion. Extensible |
| Ccore::pack::interaction_graph::SimpleInteractionGraph | A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver |
| Ccore::scoring::constraints::ConstraintGraph | |
| ►Ccore::scoring::ContextGraph | |
| Ccore::scoring::TenANeighborGraph | |
| Ccore::scoring::TwelveANeighborGraph | |
| Ccore::scoring::EnergyGraph | Class to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight. The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation. This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method |
| Ccore::scoring::MinimizationGraph | Class to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity |
| ►Ccore::io::silent::SilentStruct | |
| Ccore::import_pose::PDBSilentStruct | |
| Ccore::io::silent::BinarySilentStruct | Why this inheritance pathway? this makes no sense! |
| Ccore::io::silent::ProteinSilentStruct_Template< T > | |
| Ccore::io::silent::RigidBodySilentStruct | |
| Ccore::io::silent::RNA_SilentStruct | |
| Ccore::io::silent::ScoreFileSilentStruct | |
| Ccore::io::silent::ScoreJumpFileSilentStruct | |
| ►Ccore::kinematics::tree::Atom | Kinematics Atom interface class |
| ►Ccore::kinematics::tree::Atom_ | Kinematics Atom abstract base class |
| Ccore::kinematics::tree::BondedAtom | Atom which are bonded to its parent, derived from Atom_ |
| Ccore::kinematics::tree::JumpAtom | Atom who are connected to its parent via rigid-body transformation "Jump" |
| ►Ccore::pack::task::PackerTask | Task class that gives instructions to the packer |
| Ccore::pack::task::PackerTask_ | PackerTask controls what rotameric (including sequence) changes the packer is allowed to make |
| Ccore::pose::Pose | A molecular system including residues, kinematics, and energies |
| Ccore::scoring::hbonds::HBond | |
| ►Ccore::scoring::ScoreFunction | This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated |
| Ccore::scoring::DockingScoreFunction | |
| Ccore::scoring::MinScoreScoreFunction | |
| Ccore::scoring::symmetry::SymmetricScoreFunction | |
| CEntry | |
| Cupdate_ResidueType_enum_files.EnumInfo | |
| Ccore::scoring::etable::EtableParamsOnePair | EtableParamsOnePair 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 | |
| ►Cutility::excn::EXCN_Msg_Exception [external] | |
| ►Ccore::conformation::membrane::EXCN_Membrane | Parent Exception - Exception Membrane |
| Ccore::conformation::membrane::EXCN_Illegal_Arguments | Illegal Arguments Exception |
| Ccore::conformation::membrane::EXCN_Membrane_Bounds | Membrane Out of Bounds Exception |
| Ccore::conformation::membrane::EXCN_MembraneFoldTree | Fold tree Exception for membrane proteins |
| Ccore::conformation::membrane::EXCN_NonMembrane | Non Membrane Pose Exception |
| Ccore::conformation::membrane::EXCN_Resource_Definition | Resource Manager Exception |
| Ccore::conformation::membrane::EXCN_VirtualRsd | Virtual Residue Definition Exception |
| Ccore::environment::EXCN_Env_Exception | |
| Ccore::environment::EXCN_FTSketchGraph | |
| Ccore::id::EXCN_AtomNotFound | |
| Ccore::kinematics::EXCN_InvalidFoldTree | |
| Ccore::pack::task::ResfileReaderException | |
| Ccore::scoring::sc::ShapeComplementarityCalculatorException | |
| Ccore::pack::interaction_graph::exposed_hydrophobic_data | |
| Ccore::fragment::picking_old::concepts::Extent< PageIterator > | Forward declaration for Extent |
| Ccore::fragment::picking_old::concepts::ExtentEvaluator< Bookmark, Ext > | Forward declaration for core::fragments::picking_old::concepts::ExtentEvaluator |
| Ccore::fragment::picking_old::concepts::ExtentGenerator< Extent > | Forward declaration for core::fragment::picking_old::concepts::ExtentGenerator |
| Ccore::scoring::etable::ExtraQuadraticRepulsion | ExtraQuadraticRepulsion 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::io::pdb::FileData | FileData class. Hold data created from PDB file |
| Ccore::scoring::saxs::FormFactorManager | Selects a given number of fragments using a quota scheme |
| Ccore::fragment::FragFactory | |
| Ccore::fragment::FragID | |
| Ccore::fragment::FragmentIO | |
| Ccore::indexed_structure_store::FragmentLookupResult | |
| Ccore::indexed_structure_store::FragmentSpecification | |
| Ccore::scoring::disulfides::FullatomDisulfideEnergyComponents | |
| Ccore::scoring::disulfides::FullatomDisulfideParams13 | |
| Ccore::optimization::func_1d | |
| Ccore::scoring::func::FuncFactory | |
| ►CG | |
| ►Ccore::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | Function declarations for the AdditionalBackgroundNodesInteractionGraph |
| Ccore::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | Defines the interaction graph that will keep track of changes to the hpatch score |
| Ccore::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > | Defines the interaction graph that will keep track of changes to the surface score |
| Ccore::optimization::GA_Minimizer | |
| Ccore::chemical::rna::GaussianParameter | |
| ►Ccore::pose::signals::GeneralEvent | Signals a general change in a Pose |
| Ccore::pose::signals::ConformationEvent | Signals a conformation change in a Pose |
| Ccore::pose::signals::EnergyEvent | Signals an energy change in a Pose |
| ►Ccore::conformation::signals::GeneralEvent | Signals a general change in a Conformation |
| Ccore::conformation::signals::IdentityEvent | Signals a change in residue identity in a Conformation |
| Ccore::conformation::signals::LengthEvent | Signals a change in length of residues in a Conformation |
| Ccore::conformation::signals::XYZEvent | Signals a change in XYZ coordinates in a Conformation |
| Ccore::scoring::etable::etrie::GenericResidueConnectionData | |
| Ccore::io::pdb::GeometricRenameIsomorphismCallback | |
| Ccore::io::pdb::GeometricRenameVerticiesEquivalent | Will consider two verticies equivalent if they have the same element |
| Ccore::scoring::Hairpin | |
| Ccore::scoring::Hairpins | |
| Ccore::scoring::hbonds::hbtrie::HBAtom | |
| Ccore::scoring::hbonds::hbtrie::HBCPData | |
| Ccore::scoring::hbonds::HBEvalTuple | |
| Ccore::scoring::hbonds::HBondDerivs | |
| Ccore::scoring::hbonds::HBondTypeManager | |
| Ccore::chemical::HeavyAtomFilter | The filter responsible for obtaining all heavy atoms |
| Ccore::chemical::HeavyAtomWithHydrogensFilter | The filter responsible for finding heavy atoms with hydrogens |
| Ccore::chemical::HeavyAtomWithPolarHydrogensFilter | The filter responsible for obtaining all heavy atoms with polar hydrogens attached to them |
| Ccore::scoring::Helices | |
| Ccore::pack::interaction_graph::history_queue_struct | For storing three peices of associated data describing the recent history structure on a LinearMemNode |
| Ccore::scoring::packing::HolesParams | |
| Ccore::scoring::packing::HolesParamsRes | |
| Ccore::scoring::packstat::HTL_EventX | |
| Ccore::chemical::HydrogenAtomFilter | The filter responsible for all hydrogens |
| Ccore::chemical::ICoorAtomID | Atom 's ID in internal coordinates in a ResidueType |
| Ccore::chemical::orbitals::ICoorOrbitalData | |
| Ccore::pack::interaction_graph::InteractionGraphFactory | |
| ►Ccore::scoring::etable::count_pair::Invoker | |
| ►Ccore::scoring::etable::ResResEnergyInvoker< Evaluator > | |
| Ccore::scoring::etable::BB_BB_EnergyInvoker< Evaluator > | |
| Ccore::scoring::etable::SC_BB_EnergyInvoker< Evaluator > | |
| Ccore::scoring::etable::SC_SC_EnergyInvoker< Evaluator > | |
| Ccore::scoring::etable::SC_Whole_EnergyInvoker< Evaluator > | |
| Ccore::scoring::etable::WholeWholeEnergyInvoker< Evaluator > | |
| ►Citerator | |
| ►Ccore::fragment::ConstFrameIterator | |
| Ccore::fragment::FrameIterator | |
| Ccore::fragment::FragID_Iterator | |
| Ccore::io::raw_data::RawFileData::iterator | Iterator class for RawFileData container |
| Ccore::io::silent::SilentFileData::iterator | Iterator class for SilentFileData container |
| Ccore::optimization::JJH_Minimizer | |
| Ccore::kinematics::Jump | Object which makes rigid-body transformation with translational and rotational perturbation |
| Ccore::id::JumpID | |
| Ccore::scoring::electron_density::KromerMann | |
| Ccore::optimization::lbfgs_iteration_data | |
| Ccore::scoring::packstat::LeeRichards | |
| Ccore::environment::LengthChecker | |
| 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_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary | |
| ►Ccore::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary > | |
| Ccore::fragment::picking_old::vall::VallLibrarian | Librarian that picks fragments from the Vall |
| 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 | |
| ►Ccore::fragment::picking_old::concepts::Library< VallSections > | |
| Ccore::fragment::picking_old::vall::VallLibrary | Vall fragment library |
| Ccore::util::Line | Struct |
| Ccore::io::pdb::LinkInformation | A structure for storing information from PDB LINK records |
| Ccore::scoring::packstat::LR_AtomData | |
| Ccore::scoring::packstat::LR_MP_AtomData | |
| ►Cstd::map< K, T > | STL class |
| Ccore::scoring::motif::MotifHitStats | |
| Ccore::optimization::symmetry::MinDebug | |
| Ccore::optimization::Minimizer | Simple low-level minimizer class |
| Ccore::chemical::MMAtomType | Basic MM atom type |
| Ccore::scoring::mm::MMBondAngleResidueTypeParam | |
| Ccore::chemical::sdf::MolWriter | |
| Ccore::scoring::motif::MotifHashManager | |
| Ccore::scoring::motif::MotifHit | |
| Ccore::scoring::motif::MyHash | |
| Ccore::scoring::motif::MyPred | |
| Ccore::id::NamedAtomID | Atom identifier class |
| Ccore::id::NamedAtomID_Map< T > | Map from Atom identifiers to contained values class |
| ►Ccore::id::NamedAtomID_Map< NamedAtomID > | |
| Ccore::id::NamedAtomID_Map_NamedAtomID | |
| Ccore::id::NamedStubID | |
| Ccore::graph::NegSpaceElement< T > | NegSpaceElement represents a single element in the singly-linked list of negative space in an array pool |
| Ccore::graph::NegSpaceElement< double > | |
| Ccore::optimization::NelderMeadSimplex | |
| ►Ccore::graph::Node | |
| Ccore::pack::interaction_graph::SimpleNode | |
| Ccore::scoring::constraints::ConstraintNode | |
| Ccore::scoring::EnergyNode | |
| Ccore::scoring::MinimizationNode | |
| Ccore::scoring::TenANeighborNode | |
| Ccore::scoring::TwelveANeighborNode | |
| Ccore::kinematics::Node | |
| ►Ccore::pack::interaction_graph::NodeBase | |
| ►Ccore::pack::interaction_graph::FixedBBNode | |
| ►Ccore::pack::interaction_graph::OnTheFlyNode | |
| Ccore::pack::interaction_graph::DoubleLazyNode | |
| Ccore::pack::interaction_graph::LazyNode | |
| Ccore::pack::interaction_graph::LinearMemNode | |
| ►Ccore::pack::interaction_graph::PrecomputedPairEnergiesNode | |
| Ccore::pack::interaction_graph::DensePDNode | |
| Ccore::pack::interaction_graph::DoubleDensePDNode | |
| Ccore::pack::interaction_graph::FASTERNode | |
| Ccore::pack::interaction_graph::PDNode | |
| ►Ccore::pack::interaction_graph::SymmOnTheFlyNode | |
| Ccore::pack::interaction_graph::SymmLinearMemNode | |
| Ccore::pack::interaction_graph::SymmMinimalistNode | |
| ►Cutility::graph::null_bfs_prune_visitor [external] | |
| Ccore::chemical::RigidDistanceVisitor | Utility visitor for find_nbr_dist Will only traverse those atoms in the "rigid" portion of graph around the starting atom. "Rigid" includes direct neighbors and atoms connected by non-rotatable bonds e.g. all rings, all double/triple bonds, methyl groups, single atoms, etc |
| Ccore::scoring::packstat::Octree2D | |
| Ccore::scoring::electron_density::OneGaussianScattering | |
| Ccore::chemical::Orbital | Basic chemical atom |
| Ccore::scoring::orbitals::OrbitalsAssigned | |
| Ccore::scoring::orbitals::OrbitalsStatistics | |
| Ccore::chemical::orbitals::OrbitalType | |
| Ccore::chemical::orbitals::OrbitalTypeMapper | |
| Ccore::conformation::orbitals::OrbitalXYZCoords | |
| Ccore::scoring::packstat::OrderCavBallOnR | |
| Ccore::scoring::packstat::OrderCavBallOnRmAnb | |
| Ccore::scoring::packstat::OrderCavBallOnRmE | |
| Ccore::scoring::packstat::OrderCavBallOnX | |
| Ccore::scoring::packstat::OrderCBC | |
| Ccore::scoring::packstat::OrderSphereOnID | |
| Ccore::scoring::packstat::OrderSphereOnX | |
| Ccore::scoring::dssp::Pairing | |
| Ccore::io::pdb::PDB_DReader | PDB Reader itself, D - for dynamic approach of type handling |
| Ccore::scoring::cryst::PhenixInterface | |
| Ccore::scoring::packstat::Point | |
| ►Ccore::conformation::PointGraphEdgeData | |
| Ccore::conformation::AtomGraphEdgeData | |
| ►Ccore::conformation::PointGraphVertexData | |
| Ccore::conformation::AtomGraphVertexData | |
| Ccore::scoring::packstat::PointPair | |
| Ccore::chemical::PolarHydrogenFilter | The filter responsible for all polar hydrogens |
| ►Cnumeric::Polynomial_1d [external] | |
| Ccore::scoring::hbonds::Polynomial_1d | |
| Ccore::scoring::electron_density::poseCoord | |
| Ccore::init::pre_talaris_2013_behavior_settings | |
| Ccore::pack::dunbrack::ProbSortClass | |
| Ccore::scoring::ProQPotential | |
| Ccore::scoring::methods::PyEnergyMethodRegistrator | This 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 |
| ►Ccore::io::raw_data::RawFileData | Abstract 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 |
| Ccore::io::raw_data::DecoyFileData | |
| Ccore::io::raw_data::ScoreFileData | |
| Ccore::scoring::RDC | |
| Ccore::scoring::RDC_Rohl | |
| Ccore::chemical::RealFilter | A filtered graph that doesn't contain fake/virtual atoms and fake/virtual bonds |
| ►CReferenceCount | |
| Ccore::environment::FoldTreeSketch::Node | |
| ►Cutility::pointer::ReferenceCount [external] | |
| Ccore::graph::ArrayPool< double > | |
| Ccore::chemical::AtomTypeDatabaseIO | |
| Ccore::chemical::AtomTypeSet | Set of AtomTypes |
| Ccore::chemical::AutomorphismIterator | Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations |
| Ccore::chemical::carbohydrates::CarbohydrateInfo | |
| Ccore::chemical::Element | Stores element properties |
| Ccore::chemical::ElementSet | A set of Bcl Elements |
| Ccore::chemical::gasteiger::GasteigerAtomTypeData | |
| Ccore::chemical::gasteiger::GasteigerAtomTypeSet | A set of Bcl Atom types |
| Ccore::chemical::gasteiger::PossibleAtomTypesForAtom | A helper class by which AtomTypes can return all possible atom types for a given atom in a structure that is easily accessed by orbital type |
| Ccore::chemical::IdealBondLengthSet | A set of Elements |
| Ccore::chemical::MMAtomTypeSet | A set of MMAtomTypes |
| Ccore::chemical::orbitals::OrbitalTypeSet | |
| Ccore::chemical::Patch | A class patching basic ResidueType to create variant types, containing multiple PatchCase |
| Ccore::chemical::PatchCase | A single case of a patch, eg proline Nterminus is a case of NtermProteinFull |
| ►Ccore::chemical::PatchOperation | A single operation that needs to be applied in a residue patch |
| Ccore::chemical::AddAtom | Add an atom to ResidueType |
| Ccore::chemical::AddAtomAlias | A patch operation for adding an atom alias to a ResidueType |
| Ccore::chemical::AddBond | Add a bond to ResidueType |
| Ccore::chemical::AddBondType | A patch operation for adding a specific type of bond to a ResidueType |
| Ccore::chemical::AddChi | Add a chi angle to ResidueType |
| Ccore::chemical::AddChiRotamer | Add a rotamer sample to a chi angle of the ResidueType |
| Ccore::chemical::AddConnect | |
| Ccore::chemical::AddProperty | Add a property to ResidueType |
| Ccore::chemical::AddProtonChi | |
| Ccore::chemical::AppendInterchangeabilityGroup_String | Append a string to the existing interchangeability_group string for a ResidueType |
| Ccore::chemical::AppendMainchainAtom | Add a mainchain atom after the last mainchain atom |
| Ccore::chemical::DeleteAtom | Delete an atom |
| Ccore::chemical::DeleteProperty | Delete a property from ResidueType Added by Andy M. Chen in June 2009 This is needed for deleting properties, which occurs in certain PTM's (e.g. methylation) |
| Ccore::chemical::NCAARotLibPath | Set the path to a rotamer library for an NCAA that is not in dunbrack |
| Ccore::chemical::PrependMainchainAtom | Add a mainchain atom before the first mainchain atom |
| Ccore::chemical::RedefineChi | Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTMs |
| Ccore::chemical::SetAtomicCharge | Set an atom's charge |
| Ccore::chemical::SetAtomType | Set atom's chemical type |
| Ccore::chemical::SetBackboneHeavyatom | Set an atom as backbone heavy atom |
| Ccore::chemical::SetFormalCharge | A patch operation for setting the formal charge of a ResidueType's atom |
| Ccore::chemical::SetICoor | Set an atom's AtomICoord |
| Ccore::chemical::SetInterchangeabilityGroup_String | Set the interchangeability_group string for a ResidueType |
| Ccore::chemical::SetIO_String | Set atom's chemical type |
| Ccore::chemical::SetMMAtomType | Set atom's MM chemical type |
| Ccore::chemical::SetNbrAtom | Set the residue neighbor atom |
| Ccore::chemical::SetNbrRadius | Set the residue neighbor radius |
| Ccore::chemical::SetOrientAtom | Set orient atom selection mode |
| Ccore::chemical::SetPolymerConnectAtom | Set an atom as polymer connection |
| Ccore::chemical::ResidueDatabaseIO | |
| Ccore::chemical::ResidueProperties | |
| Ccore::chemical::ResidueSelector | A class picking out a subset of ResidueType by multiple criteria |
| ►Ccore::chemical::ResidueSelectorSingle | A base class for defining a ResidueSelector by a single criterion |
| Ccore::chemical::Selector_AA | Does the residue belong to ANY of these AAs? |
| Ccore::chemical::Selector_CMDFLAG | Is a certain string in the command-line option -chemical:allow_patch present ? this selector does actually not depend on the residuetype it is queried for |
| Ccore::chemical::Selector_MATCH_VARIANTS | Does the residue have ALL of the variant types and no more |
| Ccore::chemical::Selector_NAME1 | Does the residue belong to ANY of these one-letter codes? |
| Ccore::chemical::Selector_NAME3 | Does the residue have to ANY of these three-letter codes? |
| Ccore::chemical::Selector_NO_VARIANTS | Does the residue have NO variant types? |
| Ccore::chemical::Selector_PROPERTY | Does the residue have ANY of these properties? |
| Ccore::chemical::Selector_UPPER_POSITION | Does the main chain of this residue follow from the given position label? |
| Ccore::chemical::Selector_VARIANT_TYPE | Does the residue have ANY of variant types? |
| Ccore::chemical::ResidueType | A class for defining a type of residue |
| Ccore::chemical::ResidueTypeKinWriter | |
| Ccore::chemical::ResidueTypeSet | A collection of ResidueType defined |
| Ccore::chemical::RingConformerSet | |
| Ccore::chemical::rna::RNA_FittedTorsionInfo | |
| Ccore::chemical::rna::RNA_ResidueType | |
| Ccore::chemical::sdf::MolFileIOAtom | |
| Ccore::chemical::sdf::MolFileIOBond | |
| Ccore::chemical::sdf::MolFileIOMolecule | |
| Ccore::chemical::sdf::MolFileIOReader | |
| Ccore::coarse::CoarseEtable | |
| Ccore::coarse::Translator | |
| Ccore::coarse::TranslatorSet | |
| ►Ccore::conformation::AbstractRotamerTrie | |
| ►Ccore::scoring::trie::RotamerTrieBase | |
| Ccore::scoring::trie::RotamerTrie< AT, CPDATA > | |
| Ccore::conformation::Conformation | A container of Residues and the kinematics to manage them |
| Ccore::conformation::ConformationKinWriter | |
| Ccore::conformation::membrane::LipidAccInfo | Membrane Lipid Accessibility Data |
| Ccore::conformation::membrane::MembraneInfo | Membrane Info Object - Contains information for describing a membrane protein in Rosetta, including the position of the membrane virtual residue, spanning topology, and lips acc data |
| Ccore::conformation::membrane::Span | |
| Ccore::conformation::membrane::SpanningTopology | |
| Ccore::conformation::parametric::Parameters | Parameters class, used to store sets of parameters for parametric backbone generation |
| Ccore::conformation::parametric::ParametersSet | ParametersSet class, used to store sets of parameters for parametric backbone generation |
| Ccore::conformation::PseudoBond | |
| Ccore::conformation::PseudoBondCollection | |
| Ccore::conformation::Residue | Instance Residue class, used for placed residues and rotamers |
| Ccore::conformation::ResidueKinWriter | |
| ►Ccore::conformation::ResidueMatcher | |
| Ccore::conformation::ExactResidueMatcher | |
| Ccore::conformation::WatsonCrickResidueMatcher | |
| ►Ccore::conformation::RotamerSetBase | |
| ►Ccore::pack::rotamer_set::RotamerSet | |
| ►Ccore::pack::rotamer_set::RotamerSet_ | Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" – the rotamer present on the input pose before packing began |
| Ccore::pack::rotamer_set::symmetry::SymmetricRotamerSet_ | Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" – the rotamer present on the input pose before packing began. symmetrical version of RotamerSet_ |
| Ccore::pack::rotamer_set::RotamerSubset | Container for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It's main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the "rot_to_pack" vector) |
| Ccore::conformation::symmetry::SymmData | |
| Ccore::conformation::symmetry::SymmetryInfo | |
| Ccore::conformation::UltraLightResidue | |
| Ccore::environment::DofPassport | |
| Ccore::environment::EnvCore | |
| Ccore::environment::FoldTreeSketch | |
| Ccore::environment::LocalPosition | |
| Ccore::environment::SequenceAnnotation | |
| ►Ccore::fragment::BaseCacheUnit | |
| Ccore::fragment::MapCacheUnit< T > | |
| Ccore::fragment::VectorCacheUnit< T > | |
| Ccore::fragment::FragData | |
| Ccore::fragment::FragmentRmsd | |
| ►Ccore::fragment::FragSet | |
| Ccore::fragment::ConstantLengthFragSet | A set of fragments that contains fragments of a constant length read in from a fragment file |
| Ccore::fragment::FragSetCollection | |
| Ccore::fragment::OrderedFragSet | |
| ►Ccore::fragment::Frame | Frame couples a list of FragData-instances to a certain alignment frame, i.e., position in sequence space |
| ►Ccore::fragment::NonContinuousFrame | JumpingFrame is a discontinuous frame i.e, the SRFDs stored in the FragData objects can be applied to residues anywhere a 5 7 9 Frame of a FragData containing three BBTorsionSRFDs would change torsions of 5 7 9 a 5 32 2 Frame of a FragData containing two BBTorsionSRFD and on JumpSRFD would change torsions of 5 and 32 and the RT of jump_nr 2 note that in the latter case the 2 is not coding for a residue number! |
| Ccore::fragment::JumpingFrame | JumpingFrame, so far there is nothing special about JumpingFrames. but I think we might want to have additionally information like the start and end residues that belong to a certain jump_nr.! okay: right now I require that the creator of a JumpingFrame sets start to the start-residue of the jump |
| ►Ccore::fragment::FrameIteratorWorker_ | |
| Ccore::fragment::ConstantLengthFragSetIterator_ | |
| Ccore::fragment::FrameListIterator_ | |
| Ccore::fragment::OrderedFragSetIterator_ | |
| ►Ccore::fragment::picking_old::vall::eval::VallFragmentEval | Base class for Vall ExtentEvaluator |
| Ccore::fragment::picking_old::vall::eval::ABEGOEval | Scores a fragment based on sum of secondary structure identity and sequence identity |
| Ccore::fragment::picking_old::vall::eval::EnergyEval | Scores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction |
| Ccore::fragment::picking_old::vall::eval::IdentityEval | Scores a fragment based on sum of secondary structure identity and sequence identity |
| ►Ccore::fragment::picking_old::vall::gen::VallFragmentGen | Base class Vall ExtentGenerator |
| Ccore::fragment::picking_old::vall::gen::LengthGen | Default constant length fragment Vall ExtentGenerator |
| Ccore::fragment::picking_old::vall::gen::SecStructGen | Generator that requires fragments to have a specific secondary structure string |
| Ccore::fragment::SecondaryStructure | Tiny helper class that knows the relative fractions of secondary structure L,H,E so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, |
| ►Ccore::fragment::SingleResidueFragData | Base class for SRFD classes |
| Ccore::fragment::DownJumpSRFD | |
| ►Ccore::fragment::SecstructSRFD | |
| ►Ccore::fragment::BBTorsionSRFD | |
| Ccore::fragment::BBTorsionAndAnglesSRFD | |
| Ccore::fragment::IndependentBBTorsionSRFD | A version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD) |
| Ccore::fragment::UpJumpSRFD | |
| Ccore::fragment::TorsionInfoSet | |
| Ccore::graph::ArrayPool< T > | |
| Ccore::graph::Graph | A Graph with constant time edge insertion and deletion. Extensible |
| Ccore::graph::UEVertex< V, E > | |
| Ccore::graph::UpperEdgeGraph< V, E > | |
| Ccore::grid::CartGrid< T > | |
| ►Ccore::id::SequenceMapping | |
| Ccore::sequence::DerivedSequenceMapping | |
| Ccore::import_pose::atom_tree_diffs::AtomTreeDiff | An object wrapper for reading atom_tree_diff files, complete with embedded reference structures |
| ►Ccore::import_pose::pose_stream::PoseInputStream | |
| Ccore::import_pose::pose_stream::ExtendedPoseInputStream | |
| Ccore::import_pose::pose_stream::LazySilentFilePoseInputStream | |
| Ccore::import_pose::pose_stream::MetaPoseInputStream | |
| Ccore::import_pose::pose_stream::PDBPoseInputStream | |
| Ccore::import_pose::pose_stream::SilentFilePoseInputStream | |
| Ccore::import_pose::pose_stream::PoseOutputStream | |
| Ccore::indexed_structure_store::FragmentLookup | |
| Ccore::indexed_structure_store::FragmentStore | |
| Ccore::io::pdb::HeaderInformation | Information stored in the header records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z |
| Ccore::io::PositionDdGInfo::PositionDdGInfo | Small helper class that stores the ddGs for mutations at a given position. camel case gets weird when trying to write words containing ddG.. |
| ►Ccore::io::raw_data::RawStruct | |
| Ccore::io::raw_data::DecoyStruct | |
| Ccore::io::raw_data::ScoreStructJSON | |
| Ccore::io::raw_data::ScoreStructText | |
| Ccore::io::rna::RDAT | |
| Ccore::io::rna::RNA_DataReader | |
| ►Ccore::io::silent::SharedSilentData | |
| Ccore::io::silent::EnergyNames | |
| Ccore::io::silent::SimpleSequenceData | |
| Ccore::io::silent::SilentFileData | Abstract base class for classes that read and write different types of silent-files. Silent-files can contain SilentStruct objects which are expected, to be uniquely identified by some sort of string-based tag inside the file |
| Ccore::io::silent::SilentStruct | |
| ►Ccore::io::silent::SilentStructCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| Ccore::import_pose::PDBSilentStructCreator | Creator for the PDBSilentStruct class |
| Ccore::io::silent::BinarySilentStructCreator | Creator for the BinarySilentStruct class |
| Ccore::io::silent::ProteinSilentStruct_SinglePrecCreator | Creator for the ProteinSilentStruct_SinglePrec class |
| Ccore::io::silent::ProteinSilentStructCreator | Creator for the ProteinSilentStruct class |
| Ccore::io::silent::RigidBodySilentStructCreator | Creator for the RigidBodySilentStruct class |
| Ccore::io::silent::RNA_SilentStructCreator | Creator for the RNA_SilentStruct class |
| Ccore::io::silent::ScoreFileSilentStructCreator | Creator for the ScoreFileSilentStruct class |
| Ccore::io::silent::ScoreJumpFileSilentStructCreator | Creator for the ScoreJumpFileSilentStruct class |
| Ccore::kinematics::AtomTree | Wrapper for a tree of kinematic Atoms |
| Ccore::kinematics::FoldTree | The FoldTree is a residue-based treelike representation of a molecule |
| ►Ccore::kinematics::MinimizerMapBase | |
| Ccore::optimization::CartesianMinimizerMap | |
| Ccore::optimization::MinimizerMap | |
| Ccore::optimization::symmetry::SymMinimizerMap | Atom tree multifunction class |
| ►Ccore::pack::scmin::SCMinMinimizerMap | |
| Ccore::pack::scmin::AtomTreeSCMinMinimizerMap | |
| Ccore::pack::scmin::CartSCMinMinimizerMap | |
| Ccore::kinematics::MoveMap | A class specifying DOFs to be flexible or fixed |
| Ccore::kinematics::ResidueCoordinateChangeList | The AtomTree is responsible for informing the conformation of which residues have had either internal (DOF) or external (xyz) coordinate changes so that the Conformation may shuttle O(k) – output sensitive – data from the AtomTree to the Residue objects it manages |
| Ccore::kinematics::ShortestPathInFoldTree | |
| Ccore::kinematics::tree::Atom | Kinematics Atom interface class |
| ►Ccore::optimization::AtomTreeMinimizer | High-level atom tree minimizer class |
| Ccore::optimization::symmetry::SymAtomTreeMinimizer | High-level atom tree minimizer class |
| Ccore::optimization::CartesianMinimizer | High-level atom tree minimizer class |
| Ccore::optimization::DOF_Node | |
| ►Ccore::optimization::LineMinimizationAlgorithm | |
| Ccore::optimization::ArmijoLineMinimization | |
| Ccore::optimization::BrentLineMinimization | |
| Ccore::optimization::StrongWolfeLineMinimization | |
| Ccore::optimization::MinimizerOptions | |
| ►Ccore::optimization::Multifunc | Multifunction interface class |
| ►Ccore::optimization::AtomTreeMultifunc | Atom tree multifunction class |
| Ccore::optimization::SingleResidueMultifunc | A streamlined AtomTreeMultifunc designed specifically for RTMIN |
| Ccore::optimization::CartesianMultifunc | Atom tree multifunction class |
| Ccore::optimization::symmetry::SymAtomTreeMultifunc | Atom tree multifunction class |
| Ccore::pack::scmin::CartSCMinMultifunc | |
| Ccore::pack::scmin::SCMinMultifunc | |
| Ccore::optimization::NumericalDerivCheckResult | |
| Ccore::optimization::Particle | Simple data container for PSO algorithm |
| Ccore::optimization::ParticleSwarmMinimizer | Particle Swarm Optimization engine |
| ►Ccore::optimization::SimpleDerivCheckResult | |
| Ccore::optimization::NumDerivCheckData | |
| ►Ccore::pack::annealer::SimAnnealerBase | |
| ►Ccore::pack::annealer::RotamerAssigningAnnealer | |
| Ccore::pack::annealer::DebuggingAnnealer | |
| Ccore::pack::annealer::FASTERAnnealer | |
| Ccore::pack::annealer::FixbbCoupledRotamerSimAnnealer | |
| Ccore::pack::annealer::FixbbLinkingRotamerSimAnnealer | |
| Ccore::pack::annealer::FixbbSimAnnealer | |
| Ccore::pack::annealer::MultiCoolAnnealer | |
| Ccore::pack::dunbrack::ChiSet | |
| Ccore::pack::dunbrack::CoarseRotamer | |
| Ccore::pack::dunbrack::CoarseRotamerSet | |
| ►Ccore::pack::dunbrack::RotamerBuildingData | Simple class for passing data around in virtual function calls of the rotamer creating process. Derived classes will be simple containers for interpolated rotameric data that 1) has to be available to the derived class when building rotamers and 2) cannot be stored as member data in the derived class in a thread-safe manner. Derived classes of the RotamerBuildingData can be declared on the stack, passed into the RotamericSingleResidueDunbrackLibrary::build_chi_sets function, and then in the (virtual) chisamples_for_rotamer function, the derived classes may be downcast |
| ►Ccore::pack::dunbrack::RotamericData< T > | DOUG DOUG DOUG |
| Ccore::pack::dunbrack::BBDepSemiRotamericData< T > | A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone dependent rotamers |
| Ccore::pack::dunbrack::BBIndSemiRotamericData< T > | A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone independent rotamers |
| Ccore::pack::dunbrack::RotamerLibraryScratchSpace | |
| ►Ccore::pack::dunbrack::SingleResidueRotamerLibrary | SingleResidueRotamerLibrary pure virtual base class |
| Ccore::pack::dunbrack::cenrot::SingleResidueCenrotLibrary | |
| Ccore::pack::dunbrack::CoarseSingleResidueLibrary | |
| Ccore::pack::dunbrack::SingleLigandRotamerLibrary | A fixed library of conformations for some residue type (doesn't have to be a ligand) |
| ►Ccore::pack::dunbrack::SingleResidueDunbrackLibrary | |
| ►Ccore::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > | DOUG DOUG DOUG |
| Ccore::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > | This class is meant to represent the non-rotameric chi observed in several amino acids (asn, asp, gln, glu, his, phe, trp, tyr ) which are rotameric for the chi closest to the backbone and non rotameric for exactly one chi angle. This non-rotameric chi (abv. nrchi) is the last chi for each of these 8 amino acids except tyrosine, where this chi is the last heavy-atom chi. The last chi on tyrosine governs a hydroxyl. Unlike in the fully rotameric residues, the last heavyatom chi in semi-rotameric residues do not "communicate" to the rotameric chi. That is, in the rotameric chi, the mean chi1 value is sensitive to the chi3 value. If the third diherdal switches from trans to g+, then chi1 would shift in response. Changes to the non-rotameric chi do not effect the rotameric chi. The data structure here is good for this model but no other |
| ►Ccore::pack::dunbrack::SingleResiduePeptoidLibrary | |
| Ccore::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | |
| ►Ccore::pack::interaction_graph::InteractionGraphBase | |
| ►Ccore::pack::interaction_graph::FixedBBInteractionGraph | |
| ►Ccore::pack::interaction_graph::OnTheFlyInteractionGraph | |
| Ccore::pack::interaction_graph::DoubleLazyInteractionGraph | The double lazy interaction graph is primarily useful for multistate design where one is interested in knowing at particular edge, all of the rotamer pair energies for a particular amino acid assignment. The double lazy interaction graph is lazy in two ways: first, in delaying the computation of rotamer pair energies until they are needed, and second, in delaying the allocation of memory for rotamer pair energies until that memory is needed. The DLIG will do one of two things once it allocates space for a block of rotamer pairs: 1) In its standard operating behavior, it will leave that space allocated until the graph is destroyed, which means that the energies it stores in that block will never be computed more than once; or 2) In its alternate operating behavior, the LMIG will deallocate some of those blocks to make sure that it never uses more than some maximum amount of memory on RPEs |
| Ccore::pack::interaction_graph::LazyInteractionGraph | |
| Ccore::pack::interaction_graph::LinearMemoryInteractionGraph | |
| ►Ccore::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | |
| Ccore::pack::interaction_graph::DensePDInteractionGraph | |
| Ccore::pack::interaction_graph::DoubleDensePDInteractionGraph | |
| Ccore::pack::interaction_graph::FASTERInteractionGraph | |
| Ccore::pack::interaction_graph::PDInteractionGraph | |
| ►Ccore::pack::interaction_graph::SymmOnTheFlyInteractionGraph | |
| Ccore::pack::interaction_graph::SymmLinearMemoryInteractionGraph | |
| Ccore::pack::interaction_graph::SymmMinimalistInteractionGraph | |
| Ccore::pack::interaction_graph::InvRotamerDots | Used to determine whether the overlap between two atoms is buried or exposed |
| Ccore::pack::interaction_graph::RotamerDots | Handles sphere-sphere overlap calculations for the HPatchInteractionGraph |
| Ccore::pack::rotamer_set::ContinuousRotamerSet | |
| Ccore::pack::rotamer_set::ContinuousRotamerSets | |
| Ccore::pack::rotamer_set::RotamerCouplings | |
| Ccore::pack::rotamer_set::RotamerLinks | |
| Ccore::pack::rotamer_set::RotamerOperation | RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation |
| ►Ccore::pack::rotamer_set::RotamerSetFactory | |
| Ccore::pack::rotamer_set::symmetry::SymmetricRotamerSetFactory | |
| ►Ccore::pack::rotamer_set::RotamerSetOperation | |
| Ccore::pack::rotamer_set::AddResiduesRotamerSetOperation | Adds in rotamers from a list of Residues, |
| Ccore::pack::rotamer_set::UnboundRotamersOperation | Adds in rotamers from the "unbound" or native structure(s), pulled from one or more PDBs supplied on the command line |
| ►Ccore::pack::rotamer_set::RotamerSetsBase | |
| ►Ccore::pack::rotamer_set::FixbbRotamerSets | |
| ►Ccore::pack::rotamer_set::RotamerSets | |
| Ccore::pack::rotamer_set::symmetry::SymmetricRotamerSets | |
| Ccore::pack::rotamer_set::RotamerSubsets | |
| Ccore::pack::rotamer_set::WaterAnchorInfo | |
| Ccore::pack::scmin::AtomTreeCollection | A collection of ResidueAtomTreeCollection objects for an entire design task |
| Ccore::pack::scmin::ResidueAtomTreeCollection | The conformation::Residues and kinematics::AtomTrees for a single collection of rotamers (e.g. a RotamerSet). Each chemical::ResidueType gets its own residue/atomtree pair. A particular AtomTree/Residue pair can be set as "active" and manipulated by setter and getters for either the coordinates of the Residues or the chi dihedrals of the AtomTree |
| Ccore::pack::scmin::ResidueAtomTreeCollectionMomento | Class to save the state for a ResidueAtomTreeCollection |
| Ccore::pack::scmin::SidechainStateAssignment | A simple class for tracking a network state and its energy where each sidechain's state is described by a series of chi angles |
| Ccore::pack::task::IGEdgeReweightContainer | Class that interfaces to containers holding IGedge weights between individual residues of the task |
| Ccore::pack::task::IGEdgeReweighter | Helper class for IGEdgeReweightContainer |
| ►Ccore::pack::task::operation::ResFilter | |
| ►Ccore::pack::task::operation::ChainIs | |
| Ccore::pack::task::operation::ChainIsnt | |
| ►Ccore::pack::task::operation::ResFilterComposition | |
| Ccore::pack::task::operation::AllResFilter | |
| Ccore::pack::task::operation::AnyResFilter | |
| Ccore::pack::task::operation::NoResFilter | |
| ►Ccore::pack::task::operation::ResidueHasProperty | |
| Ccore::pack::task::operation::ResidueLacksProperty | |
| ►Ccore::pack::task::operation::ResidueIndexIs | |
| Ccore::pack::task::operation::ResidueIndexIsnt | |
| ►Ccore::pack::task::operation::ResidueName3Is | |
| Ccore::pack::task::operation::ResidueName3Isnt | |
| ►Ccore::pack::task::operation::ResiduePDBIndexIs | |
| Ccore::pack::task::operation::ResiduePDBIndexIsnt | |
| ►Ccore::pack::task::operation::ResiduePDBInfoHasLabel | |
| Ccore::pack::task::operation::ResiduePDBInfoLacksLabel | |
| Ccore::pack::task::operation::ResidueTypeFilter | |
| ►Ccore::pack::task::operation::ResFilterCreator | The ResFilterCreator class's responsibilities are to create on demand a new ResFilter class. The ResFilterCreator must register itself with the ResFilterFactory at load time (before main() begins) so that the ResFilterFactory is ready to start creating ResFilters by the time any protocol requests one |
| Ccore::pack::task::operation::AllResFilterCreator | |
| Ccore::pack::task::operation::AnyResFilterCreator | |
| Ccore::pack::task::operation::ChainIsCreator | |
| Ccore::pack::task::operation::ChainIsntCreator | |
| Ccore::pack::task::operation::NoResFilterCreator | |
| Ccore::pack::task::operation::ResidueHasPropertyCreator | |
| Ccore::pack::task::operation::ResidueIndexIsCreator | |
| Ccore::pack::task::operation::ResidueIndexIsntCreator | |
| Ccore::pack::task::operation::ResidueLacksPropertyCreator | |
| Ccore::pack::task::operation::ResidueName3IsCreator | |
| Ccore::pack::task::operation::ResidueName3IsntCreator | |
| Ccore::pack::task::operation::ResiduePDBIndexIsCreator | |
| Ccore::pack::task::operation::ResiduePDBIndexIsntCreator | |
| Ccore::pack::task::operation::ResiduePDBInfoHasLabelCreator | |
| Ccore::pack::task::operation::ResiduePDBInfoLacksLabelCreator | |
| Ccore::pack::task::operation::ResidueTypeFilterCreator | |
| ►Ccore::pack::task::operation::ResLvlTaskOperation | |
| Ccore::pack::task::operation::AddBehaviorRLT | |
| Ccore::pack::task::operation::DisallowIfNonnativeRLT | |
| Ccore::pack::task::operation::PreventRepackingRLT | |
| Ccore::pack::task::operation::RestrictAbsentCanonicalAASRLT | |
| Ccore::pack::task::operation::RestrictToRepackingRLT | |
| ►Ccore::pack::task::operation::ResLvlTaskOperationCreator | The ResLvlTaskOperationCreator class's responsibilities are to create on demand a new ResLvlTaskOperation class. The ResLvlTaskOperationCreator must register itself with the ResLvlTaskOperationFactory at load time (before main() begins) so that the ResLvlTaskOperationFactory is ready to start creating ResLvlTaskOperations by the time any protocol requests one |
| Ccore::pack::task::operation::AddBehaviorRLTCreator | |
| Ccore::pack::task::operation::DisallowIfNonnativeRLTCreator | |
| Ccore::pack::task::operation::PreventRepackingRLTCreator | |
| Ccore::pack::task::operation::RestrictAbsentCanonicalAASRLTCreator | |
| Ccore::pack::task::operation::RestrictToRepackingRLTCreator | |
| ►Ccore::pack::task::operation::TaskOperation | |
| Ccore::pack::task::operation::AppendResidueRotamerSet | Apply rotamerSetOperation to only the rotamerSet for the given residue |
| Ccore::pack::task::operation::AppendRotamer | When a PackerTask is created by the Factory, the RotamerOperation will be given to it |
| Ccore::pack::task::operation::AppendRotamerSet | When a PackerTask is created by the Factory, the RotamerSetOperation will be given to it |
| Ccore::pack::task::operation::DisallowIfNonnative | DisallowIfNonnative allows you to define what residues are NOT allowed in packing unless that residue is present in the input. Behaves like RestrictAbsentCanonicalAAS and NOTAA except will allow a resitricted residue at a position if it is there to begin with at the time of Task creation. Will do all residues unless otherwise defined by selection syntax below |
| Ccore::pack::task::operation::DockingNoRepack1 | |
| Ccore::pack::task::operation::DockingNoRepack2 | |
| Ccore::pack::task::operation::ExtraChiCutoff | ExtraChiCutoff (correponding to flag "-extrachi_cutoff <float>" ) |
| Ccore::pack::task::operation::ExtraRotamers | ExtraRotamer for a residue. You know, -ex1, -ex2, all that |
| Ccore::pack::task::operation::ExtraRotamersGeneric | |
| Ccore::pack::task::operation::IncludeCurrent | |
| Ccore::pack::task::operation::InitializeExtraRotsFromCommandline | |
| Ccore::pack::task::operation::InitializeFromCommandline | |
| Ccore::pack::task::operation::NoRepackDisulfides | Prevent disulfides from being repacked; assume disulfides info in Pose is up-to-date |
| Ccore::pack::task::operation::OperateOnCertainResidues | |
| Ccore::pack::task::operation::OperateOnResidueSubset | |
| Ccore::pack::task::operation::OptCysHG | Run optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides() |
| Ccore::pack::task::operation::OptH | Run optH; disallowed positions may be set to prevent optimization for those residues |
| Ccore::pack::task::operation::PreserveCBeta | |
| Ccore::pack::task::operation::PreventRepacking | PreventRepacking allows you to prevent repacking (NATRO behavior) through the Factory. Useful if you do not know the residue numbers when the resfile is created. Note that this is unlike RestrictToRepacking; you have to specify which residues. If PreventRepacking worked on the entire Task you'd have a do-nothing task |
| ►Ccore::pack::task::operation::ReadResfile | |
| Ccore::pack::task::operation::ReadResfileAndObeyLengthEvents | Written by flo, feb 2011 class that can apply a resfile to a pose that had its length changed at some point in a protocol. A LengthEventCollector must be set in the pose's observer cache for this to work properly |
| Ccore::pack::task::operation::ReplicateTask | |
| Ccore::pack::task::operation::RestrictAbsentCanonicalAAS | |
| Ccore::pack::task::operation::RestrictResidueToRepacking | RestrictResidueToRepacking |
| Ccore::pack::task::operation::RestrictToInterface | |
| Ccore::pack::task::operation::RestrictToRepacking | |
| Ccore::pack::task::operation::RestrictYSDesign | RestrictYSDesign restricts positions to a binary Tyr/Ser alphabet |
| Ccore::pack::task::operation::RotamerExplosion | Rotamer explosion for a residue |
| Ccore::pack::task::operation::SetRotamerCouplings | |
| Ccore::pack::task::operation::SetRotamerLinks | |
| ►Ccore::pack::task::operation::TaskOperationCreator | The TaskOperationCreator class's responsibilities are to create on demand a new TaskOperation class. The TaskOperationCreator must register itself with the TaskOperationFactory at load time (before main() begins) so that the TaskOperationFactory is ready to start creating TaskOperations by the time any protocol requests one |
| Ccore::pack::task::operation::AppendResidueRotamerSetCreator | |
| Ccore::pack::task::operation::AppendRotamerCreator | |
| Ccore::pack::task::operation::AppendRotamerSetCreator | |
| Ccore::pack::task::operation::DisallowIfNonnativeCreator | |
| Ccore::pack::task::operation::ExtraChiCutoffCreator | |
| Ccore::pack::task::operation::ExtraRotamersCreator | |
| Ccore::pack::task::operation::ExtraRotamersGenericCreator | |
| Ccore::pack::task::operation::IncludeCurrentCreator | |
| Ccore::pack::task::operation::InitializeExtraRotsFromCommandlineCreator | |
| Ccore::pack::task::operation::InitializeFromCommandlineCreator | |
| Ccore::pack::task::operation::NoRepackDisulfidesCreator | |
| Ccore::pack::task::operation::OperateOnCertainResiduesCreator | |
| Ccore::pack::task::operation::OperateOnResidueSubsetCreator | |
| Ccore::pack::task::operation::OptCysHGCreator | |
| Ccore::pack::task::operation::OptHCreator | |
| Ccore::pack::task::operation::PreserveCBetaCreator | |
| Ccore::pack::task::operation::PreventRepackingCreator | |
| Ccore::pack::task::operation::ReadResfileAndObeyLengthEventsCreator | |
| Ccore::pack::task::operation::ReadResfileCreator | |
| Ccore::pack::task::operation::ReplicateTaskCreator | |
| Ccore::pack::task::operation::RestrictAbsentCanonicalAASCreator | |
| Ccore::pack::task::operation::RestrictResidueToRepackingCreator | |
| Ccore::pack::task::operation::RestrictToRepackingCreator | |
| Ccore::pack::task::operation::RestrictYSDesignCreator | |
| Ccore::pack::task::operation::RotamerExplosionCreator | |
| Ccore::pack::task::operation::SetRotamerCouplingsCreator | |
| Ccore::pack::task::operation::SetRotamerLinksCreator | |
| Ccore::pack::task::PackerTask | Task class that gives instructions to the packer |
| ►Ccore::pack::task::ResfileCommand | Abstract/interface class for Resfile reader command objects |
| Ccore::pack::task::ALLAA | ALLAA is deprecated; allows repacking and designing to any canonical residue (default state of PackerTask) |
| Ccore::pack::task::ALLAAwc | Allows repacking and designing to any canonical residue (default state of PackerTask) |
| Ccore::pack::task::ALLAAxc | ALLAAxc allows repacking and designing to any canonical noncysteine residue |
| Ccore::pack::task::APOLA | APOLA is deprecated, it calls APOLAR to allow nonpolar residues and packing |
| Ccore::pack::task::APOLAR | APOLAR allows nonpolar residues and packing |
| Ccore::pack::task::AUTO | AUTO suggests that a packer can/should reconsider the design setting at a/each residue |
| Ccore::pack::task::EMPTY | EMPTY disallows all canonical and noncanonical residues |
| Ccore::pack::task::EX | EX handles the various extrachi options |
| Ccore::pack::task::EX_CUTOFF | EX_CUTOFF allows setting of the extrachi_cutoff (for determining burial for extra rotamers) |
| Ccore::pack::task::FIX_HIS_TAUTOMER | FIX_HIS_TAUTOMER: when a histidine is present when the PackerTask is initialized, this flag will fix its tautomer (whether its hydrogen is on ND1 or NE2. Does nothing if not histidine at initialization (meaning if it mutates to histidine later this flag will have no effect) |
| Ccore::pack::task::NATAA | NATAA allows repacking but no sequence changes (all rotamers are of the original residue) |
| Ccore::pack::task::NATRO | NATRO disables packing and designing at a position, the residue will be totally unchanged |
| Ccore::pack::task::NC | NC handles explicit allowance of noncanonical residue types |
| Ccore::pack::task::NO_ADDUCTS | NO_ADDUCTS will disable adducts, assuming they exist This command exists because if adducts exist, then they are enabled by default for all residues |
| Ccore::pack::task::NOTAA | NOTAA disallows residues specified in a following string, and allows packing |
| Ccore::pack::task::PIKAA | PIKAA allows residues specifed in a following string and packing |
| Ccore::pack::task::PIKNA | PIKNA allows nucleic acid residues specifed in a following string |
| Ccore::pack::task::PIKRNA | PIKRNA allows nucleic acid residues specifed in a following string |
| Ccore::pack::task::POLAR | POLAR allows polar residues and packing |
| Ccore::pack::task::RESET | RESET restores the list of allowd residue types to the CAAs |
| Ccore::pack::task::SCAN | SCAN suggests to some packing routines that if there are multiple type choices for this residue, then each of them should be considered explicitly in one way or another |
| Ccore::pack::task::TARGET | TARGET flags the position as "targeted", and can optionally specify a "targeted" type |
| Ccore::pack::task::USE_INPUT_SC | USE_INPUT_SC turns on inclusion of the current rotamer for the packer |
| Ccore::pack::task::ResfileContents | |
| ►Ccore::pack::task::residue_selector::ResidueSelector | |
| Ccore::pack::task::residue_selector::AndResidueSelector | The AndResidueSelector combines the output of multiple ResidueSelectors using AND logic, i.e., only residues selected by ALL contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through add_residue_selector |
| Ccore::pack::task::residue_selector::ChainSelector | |
| Ccore::pack::task::residue_selector::ClashBasedRepackShellSelector | |
| Ccore::pack::task::residue_selector::InterGroupInterfaceByVectorSelector | The InterGroupInterfaceByVectorSelector identifies residues at the interface between two groups of residues using two distance cutoffs: the first, shorter cutoff is based on atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the residues in the first group point toward the c-alphas of the other group. Each group may be specified either explicitly through a std::set of residue indices, through a string of comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue 13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset |
| Ccore::pack::task::residue_selector::JumpDownstreamSelector | The JumpDownstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which lie downstream of a given jump in the FoldTree. The jump is specified by an integer index |
| Ccore::pack::task::residue_selector::JumpUpstreamSelector | The JumpUpstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which lie upstream of a given jump in the FoldTree. The jump is specified by its integer index |
| Ccore::pack::task::residue_selector::NeighborhoodResidueSelector | The NeighborhoodResidueSelector selects residues neighboring a defined set of residues (the focus). The focus residue set can be obtained from another ResidueSelector, from a std::set of residue positions or from a string specifying residue positions |
| Ccore::pack::task::residue_selector::NotResidueSelector | The NotResidueSelector negates the input of one loaded ResidueSelector, i.e., it is a logical NOT - it selects all unselected residues and deselects the selected ones. True becomes false, false becomes true. The ResidueSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for ResidueSelectors known to the ResidueSelectorFactory or programmatically using set_residue_selector. Note that since most ResidueSelectors clear the input ResidueSubset, NOT can be thought of as simply selecting the opposite of the passed in selector |
| Ccore::pack::task::residue_selector::NumNeighborsSelector | |
| Ccore::pack::task::residue_selector::OrResidueSelector | The OrResidueSelector combines the output of multiple ResidueSelectors using OR logic, i.e., residues selected by ANY of the contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through add_residue_selector |
| Ccore::pack::task::residue_selector::ResidueIndexSelector | The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally |
| Ccore::pack::task::residue_selector::TrueResidueSelector | |
| ►Ccore::pack::task::residue_selector::ResidueSelectorCreator | |
| Ccore::pack::task::residue_selector::AndResidueSelectorCreator | |
| Ccore::pack::task::residue_selector::ChainSelectorCreator | |
| Ccore::pack::task::residue_selector::ClashBasedRepackShellSelectorCreator | |
| Ccore::pack::task::residue_selector::InterGroupInterfaceByVectorSelectorCreator | |
| Ccore::pack::task::residue_selector::JumpDownstreamSelectorCreator | |
| Ccore::pack::task::residue_selector::JumpUpstreamSelectorCreator | |
| Ccore::pack::task::residue_selector::NeighborhoodResidueSelectorCreator | |
| Ccore::pack::task::residue_selector::NotResidueSelectorCreator | |
| Ccore::pack::task::residue_selector::NumNeighborsSelectorCreator | |
| Ccore::pack::task::residue_selector::OrResidueSelectorCreator | |
| Ccore::pack::task::residue_selector::ResidueIndexSelectorCreator | |
| Ccore::pack::task::residue_selector::TrueResidueSelectorCreator | |
| Ccore::pack::task::rna::RNA_ResidueLevelTask | |
| Ccore::pack::task::TaskFactory | Factory class for the creation and initialization of PackerTask objects |
| Ccore::pose::copydofs::CopyDofs | |
| ►Ccore::pose::datacache::CacheableObserver | Base class for Pose/Conformation observers that are stored in a Pose's DataCache |
| Ccore::pose::datacache::LengthEventCollector | Cacheable observer that keeps track of what length events occured |
| Ccore::pose::datacache::SpecialSegmentsObserver | Observer that tracks the fate of a one or more segments (i.e. pose residues) of interest. note: the convention should be that a segment.second marks the end of the segment but is not part of it, i.e. the last position of a segment is segment.second - 1 reason: some peculiar stuff regarding the meaning of length events |
| Ccore::pose::full_model_info::FullModelParameters | |
| ►Ccore::pose::metrics::PoseMetricCalculator | |
| ►Ccore::pose::metrics::EnergyDependentCalculator | |
| Ccore::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator | |
| ►Ccore::pose::metrics::StructureDependentCalculator | |
| ►Ccore::pose::metrics::simple_calculators::InterfaceDefinitionCalculator | |
| Ccore::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator | |
| Ccore::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator | |
| Ccore::pose::metrics::simple_calculators::SasaCalculator2 | |
| Ccore::pose::metrics::simple_calculators::SasaCalculatorLegacy | |
| Ccore::pose::metrics::PoseMetricContainer | Container for managing PoseMetricCalculators |
| Ccore::pose::MiniPose | Lightweight version of the pose with stuff I need |
| Ccore::pose::PDBInfo | Maintains pdb residue & atom information inside a Pose |
| Ccore::pose::PDBPoseMap | PDBPoseMap can be queried with PDB information (chain, sequence position) and returns a pose's resid position. Useful for handing input/output in terms of PDB positions. Can be tucked into the pose for repeated access, or generated just-in-time for a single use. Basically a wrapper class for std::map |
| Ccore::pose::Pose | A molecular system including residues, kinematics, and energies |
| Ccore::pose::Remarks | |
| Ccore::pose::rna::RNA_IdealCoord | |
| Ccore::pose::rna::RNA_SuiteName | |
| Ccore::scoring::APBSConfig | |
| Ccore::scoring::APBSConfig::I_PARAM | |
| Ccore::scoring::APBSConfig::R_PARAM | |
| Ccore::scoring::APBSResult | |
| Ccore::scoring::APBSWrapper | |
| Ccore::scoring::AtomVDW | |
| Ccore::scoring::carbon_hbonds::CarbonHBondPotential | |
| Ccore::scoring::CenHBPotential | |
| Ccore::scoring::CenRotEnvPairPotential | |
| ►Ccore::scoring::constraints::Constraint | Actually a restraint, like a virtual rubber band between a pair of atoms |
| Ccore::pack::dunbrack::DunbrackConstraint | |
| Ccore::pack::dunbrack::RotamerConstraint | This class favors a particular rotamer at a particular position by reducing its Dunbrack energy |
| Ccore::scoring::constraints::AmbiguousNMRDistanceConstraint | |
| Ccore::scoring::constraints::AngleConstraint | An Angular Constraint |
| ►Ccore::scoring::constraints::AtomPairConstraint | |
| Ccore::scoring::constraints::NamedAtomPairConstraint | |
| Ccore::scoring::constraints::BackboneStubConstraint | This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location |
| Ccore::scoring::constraints::BackboneStubLinearConstraint | This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location |
| Ccore::scoring::constraints::BigBinConstraint | Constraint on dihedral angle formed by 4 points |
| Ccore::scoring::constraints::ConstantConstraint | A Constant Constraint |
| Ccore::scoring::constraints::CoordinateConstraint | |
| Ccore::scoring::constraints::DihedralConstraint | Constraint on dihedral angle formed by 4 points |
| Ccore::scoring::constraints::DihedralPairConstraint | Constraint on dihedral angle formed by 4 points |
| Ccore::scoring::constraints::DistancePairConstraint | Constraint on CA distance |
| Ccore::scoring::constraints::LocalCoordinateConstraint | |
| ►Ccore::scoring::constraints::MultiConstraint | |
| ►Ccore::scoring::constraints::AmbiguousConstraint | Nested constraint where only the one with lowest energy is considered |
| Ccore::scoring::constraints::SiteConstraint | |
| Ccore::scoring::constraints::SiteConstraintResidues | |
| Ccore::scoring::constraints::AmbiguousNMRConstraint | |
| Ccore::scoring::constraints::FabConstraint | |
| Ccore::scoring::constraints::KofNConstraint | |
| Ccore::scoring::constraints::NonResidueTypeConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| Ccore::scoring::constraints::ResidueTypeConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| Ccore::scoring::constraints::ResidueTypeLinkingConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| Ccore::scoring::constraints::SequenceProfileConstraint | |
| ►Ccore::scoring::constraints::ConstraintCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| Ccore::pack::dunbrack::DunbrackConstraintCreator | Mover creator for the DunbrackConstraint constraint |
| Ccore::scoring::constraints::AmbiguousConstraintCreator | Mover creator for the AmbiguousConstraint constraint |
| Ccore::scoring::constraints::AmbiguousNMRConstraintCreator | Mover creator for the AmbiguousNMRConstraint constraint |
| Ccore::scoring::constraints::AmbiguousNMRDistanceConstraintCreator | Mover creator for the AmbiguousNMRDistanceConstraint constraint |
| Ccore::scoring::constraints::AngleConstraintCreator | Mover creator for the AngleConstraint constraint |
| Ccore::scoring::constraints::AtomPairConstraintCreator | Mover creator for the AtomPairConstraint constraint |
| Ccore::scoring::constraints::BigBinConstraintCreator | Mover creator for the BigBinConstraint constraint |
| Ccore::scoring::constraints::CoordinateConstraintCreator | Mover creator for the CoordinateConstraint constraint |
| Ccore::scoring::constraints::DihedralConstraintCreator | Mover creator for the DihedralConstraint constraint |
| Ccore::scoring::constraints::DihedralPairConstraintCreator | Constraint creator for DihedralPairConstraint |
| Ccore::scoring::constraints::FabConstraintCreator | Mover creator for the FabConstraint constraint |
| Ccore::scoring::constraints::KofNConstraintCreator | Mover creator for the KofNConstraint constraint |
| Ccore::scoring::constraints::LocalCoordinateConstraintCreator | Mover creator for the LocalCoordinateConstraint constraint |
| Ccore::scoring::constraints::MultiConstraintCreator | Mover creator for the MultiConstraint constraint |
| Ccore::scoring::constraints::SequenceProfileConstraintCreator | Constraint creator for the SequenceProfileConstraint constraint |
| Ccore::scoring::constraints::SiteConstraintCreator | Mover creator for the SiteConstraint constraint |
| Ccore::scoring::constraints::SiteConstraintResiduesCreator | Mover creator for the SiteConstraintResidues constraint |
| Ccore::scoring::constraints::Constraints | |
| Ccore::scoring::constraints::ConstraintSet | |
| Ccore::scoring::constraints::DOF_Constraint | This isn't quite a standard constraint since it acts on DOF's directly rather than on XYZ coordinates |
| Ccore::scoring::constraints::Obsolet_NamedAtomPairConstraint | |
| Ccore::scoring::constraints::ResidueConstraints | |
| Ccore::scoring::custom_pair_distance::AtomPairFuncList | |
| Ccore::scoring::DimerPairing | |
| Ccore::scoring::disulfides::CentroidDisulfidePotential | |
| Ccore::scoring::disulfides::DisulfideMatchingPotential | |
| Ccore::scoring::disulfides::FullatomDisulfidePotential | |
| Ccore::scoring::dna::DirectReadoutPotential | 1st pass implementation of Kono + Sarai's protein-DNA interaction potential |
| Ccore::scoring::dna::DNA_BasePotential | |
| Ccore::scoring::dna::DNABFormPotential | |
| Ccore::scoring::dna::DNATorsionPotential | |
| Ccore::scoring::dna::TorsionFourierComponent | |
| Ccore::scoring::dssp::StrandPairingSet | |
| Ccore::scoring::elec::GroupElec | |
| Ccore::scoring::electron_density::ElectronDensity | |
| ►Ccore::scoring::Energies | A cached energies object |
| Ccore::scoring::solid_surface::SurfaceEnergies | |
| Ccore::scoring::symmetry::SymmetricEnergies | |
| ►Ccore::scoring::EnvPairPotential | |
| Ccore::scoring::membrane::MembraneData | Mmebrane Data Class |
| Ccore::scoring::Membrane_FAPotential | Mmebrane Fullatom Potential - Scoring Class |
| Ccore::scoring::MembranePotential | Rosetta Membrane Low Resolution Scoring Methods |
| Ccore::scoring::etable::coulomb::Coulomb | |
| ►Ccore::scoring::etable::count_pair::CountPairFunction | |
| Ccore::scoring::etable::count_pair::CountPairAll | |
| ►Ccore::scoring::etable::count_pair::CountPairCrossover3 | |
| Ccore::scoring::etable::count_pair::CountPairIntraResC3 | |
| ►Ccore::scoring::etable::count_pair::CountPairCrossover4 | |
| Ccore::scoring::etable::count_pair::CountPairIntraResC4 | |
| Ccore::scoring::etable::count_pair::CountPairGeneric | |
| Ccore::scoring::etable::count_pair::CountPairNone | |
| ►Ccore::scoring::etable::Etable | Class definition for Etable |
| Ccore::scoring::etable::MembEtable | Jk Class definition for Etable |
| Ccore::scoring::etable::MembEtable | Jk Class definition for Etable |
| ►Ccore::scoring::etable::EtableEvaluator | |
| Ccore::scoring::etable::AnalyticEtableEvaluator | |
| Ccore::scoring::etable::TableLookupEvaluator | |
| Ccore::scoring::etable::EtableOptions | |
| Ccore::scoring::FACTSPotential | |
| Ccore::scoring::FACTSResidueInfo | |
| Ccore::scoring::FACTSRsdTypeInfo | |
| ►Ccore::scoring::func::Func | Func is an abstract base class representing a function used to define constraints, in which func(r) gives the constraint score for the given value r |
| ►Ccore::scoring::constraints::BoundFunc | |
| Ccore::scoring::constraints::OffsetPeriodicBoundFunc | Variant of the bound func that is periodic |
| Ccore::scoring::constraints::PeriodicBoundFunc | Variant of the bound func that is periodic |
| Ccore::scoring::custom_pair_distance::DistanceFunc | |
| Ccore::scoring::disulfides::CaCbCb_Angle_Func | |
| Ccore::scoring::disulfides::CaCbCbCa_Dihedral_Func | |
| Ccore::scoring::disulfides::CB_Angle_Func | |
| Ccore::scoring::disulfides::Cb_Distance_Func | Score based on the distance between Cb |
| Ccore::scoring::disulfides::CBSG_Dihedral_Func | |
| Ccore::scoring::disulfides::Cen_Distance_Func | |
| Ccore::scoring::disulfides::NCaCaC_Dihedral_Func | |
| Ccore::scoring::disulfides::SG_Dist_Func | |
| Ccore::scoring::disulfides::SGSG_Dihedral_Func | |
| Ccore::scoring::func::AmberPeriodicFunc | Function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) |
| Ccore::scoring::func::CharmmPeriodicFunc | Function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) |
| Ccore::scoring::func::CircularGeneral1D_Func | Function that allows return of arbitrary FArrays – this time circularized |
| Ccore::scoring::func::CircularHarmonicFunc | Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints |
| Ccore::scoring::func::CircularPowerFunc | Generalization of CircularCircularPowerFunc – other exponents allowed |
| Ccore::scoring::func::CircularSigmoidalFunc | Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints |
| Ccore::scoring::func::ConstantFunc | Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation |
| Ccore::scoring::func::CountViolFunc | |
| Ccore::scoring::func::EtableFunc | Class for representing arbitrarily defined functions |
| Ccore::scoring::func::FadeFunc | |
| Ccore::scoring::func::FlatHarmonicFunc | |
| Ccore::scoring::func::GaussianChainDoubleFunc | |
| Ccore::scoring::func::GaussianChainFunc | |
| Ccore::scoring::func::GaussianChainQuadrupleFunc | |
| Ccore::scoring::func::GaussianChainSingleFunc | |
| Ccore::scoring::func::GaussianChainTripleFunc | |
| Ccore::scoring::func::GaussianFunc | Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation |
| Ccore::scoring::func::HarmonicFunc | |
| Ccore::scoring::func::IdentityFunc | |
| Ccore::scoring::func::KarplusFunc | Function that evaluates a J-coupling from dihedral angles in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints |
| Ccore::scoring::func::LinearPenaltyFunction | |
| Ccore::scoring::func::MinMultiHarmonicFunc | |
| Ccore::scoring::func::MixtureFunc | Derived class of class Func representing a Mixture of several distinct functions. The function is of the form ln( g(r) / h(r) ), where g(r) is a mixture of a Gaussian and Exponential distributions, and h(r) is a Gaussian distribution. See methods and implementation for more information |
| Ccore::scoring::func::PeriodicFunc | Function of type y = ( k * cos(n * (x - x0) ) ) + C |
| Ccore::scoring::func::ScalarWeightedFunc | |
| Ccore::scoring::func::SigmoidFunc | |
| Ccore::scoring::func::SkipViolFunc | |
| Ccore::scoring::func::SoedingFunc | Derived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation |
| Ccore::scoring::func::SOGFunc | Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation |
| Ccore::scoring::func::SplineFunc | |
| Ccore::scoring::func::SquareWell2Func | |
| Ccore::scoring::func::SquareWellFunc | |
| Ccore::scoring::func::SumFunc | |
| Ccore::scoring::func::TopOutFunc | |
| Ccore::scoring::func::USOGFunc | Unnormalized, unbounded sum of Gaussians constraint |
| Ccore::scoring::methods::LK_SigmoidalFunc | |
| Ccore::scoring::func::SOGFunc_Impl | Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation |
| Ccore::scoring::GenBornPotential | |
| Ccore::scoring::GenBornResidueInfo | |
| Ccore::scoring::geometric_solvation::DatabaseOccSolEne | |
| Ccore::scoring::geometric_solvation::GeometricSolEnergyEvaluator | |
| Ccore::scoring::hbonds::FadeInterval | Classic FadeInterval |
| Ccore::scoring::hbonds::HBond | |
| Ccore::scoring::hbonds::HBondDatabase | |
| Ccore::scoring::hbonds::HBondOptions | |
| Ccore::scoring::interface_::DDPlookup | |
| Ccore::scoring::loop_graph::Loop | |
| Ccore::scoring::loop_graph::LoopCycle | |
| Ccore::scoring::loop_graph::LoopGraph | |
| Ccore::scoring::loop_graph::LoopScoreInfo | |
| ►Ccore::scoring::LREnergyContainer | |
| Ccore::scoring::constraints::CstEnergyContainer | |
| Ccore::scoring::DenseEnergyContainer | |
| Ccore::scoring::disulfides::CentroidDisulfideEnergyContainer | |
| Ccore::scoring::disulfides::DisulfideMatchingEnergyContainer | |
| Ccore::scoring::disulfides::FullatomDisulfideEnergyContainer | |
| Ccore::scoring::OneToAllEnergyContainer | |
| Ccore::scoring::PeptideBondedEnergyContainer | |
| ►Ccore::scoring::methods::CartBondedParameters | |
| Ccore::scoring::methods::BBDepCartBondedParameters | |
| Ccore::scoring::methods::BBIndepCartBondedParameters | |
| Ccore::scoring::methods::dfire::DFIRE_Potential | |
| ►Ccore::scoring::methods::EnergyMethod | Base class for the energy method hierarchy |
| ►Ccore::scoring::methods::OneBodyEnergy | |
| ►Ccore::scoring::methods::ContextDependentOneBodyEnergy | |
| Ccore::pack::interaction_graph::HPatchEnergy | Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. The difference from this energy method from the plain SurfaceEnergy method is that it calculates the patch area using methods in sasa.cc instead of using average values. This new method also uses a new approach for finding which residues to include in a patch, not just all residues within 10A |
| Ccore::pack::interaction_graph::SurfaceEnergy | Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms |
| Ccore::scoring::geometric_solvation::ExactOccludedHbondSolEnergy | |
| Ccore::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody | |
| Ccore::scoring::membrane::FaMPEnvEnergy | Fullatom Membrane Environment Energy |
| Ccore::scoring::membrane::FaMPEnvSmoothEnergy | Fullatom Membrane Solvation Energy - Statistically Derived, and smoothed derivatives |
| Ccore::scoring::membrane::MPCbetaEnergy | Membrane Environemnt CBeta Energy Term |
| Ccore::scoring::membrane::MPEnvEnergy | Mmebrane Environemnt Energy Term |
| Ccore::scoring::membrane::MPNonHelixPenalty | Class Membrane Non Helix Penalty |
| Ccore::scoring::membrane::MPTerminiPenalty | Class Membrane Termini Penalty |
| Ccore::scoring::methods::BurialEnergy | |
| Ccore::scoring::methods::CenRotEnvEnergy | |
| Ccore::scoring::methods::EnvEnergy | |
| Ccore::scoring::methods::EnvSmoothEnergy | |
| Ccore::scoring::methods::Fa_MbenvEnergy | |
| Ccore::scoring::methods::MembraneCbetaEnergy | |
| Ccore::scoring::methods::MembraneEnvEnergy | |
| Ccore::scoring::methods::MembraneEnvSmoothEnergy | |
| Ccore::scoring::methods::SmoothEnvEnergy | |
| Ccore::scoring::nv::NVscore | |
| ►Ccore::scoring::methods::ContextIndependentOneBodyEnergy | |
| Ccore::pack::dunbrack::cenrot::CenRotDunEnergy | |
| Ccore::pack::dunbrack::DunbrackEnergy | |
| Ccore::scoring::dna::DNAChiEnergy | |
| Ccore::scoring::methods::FreeDOF_Energy | |
| Ccore::scoring::methods::NMerPSSMEnergy | |
| Ccore::scoring::methods::NMerRefEnergy | |
| Ccore::scoring::methods::NMerSVMEnergy | |
| Ccore::scoring::methods::OmegaTetherEnergy | |
| Ccore::scoring::methods::P_AA_Energy | |
| Ccore::scoring::methods::P_AA_pp_Energy | |
| Ccore::scoring::methods::pHEnergy | |
| Ccore::scoring::methods::RamachandranEnergy | |
| Ccore::scoring::methods::ReferenceEnergy | |
| Ccore::scoring::methods::ReferenceEnergyNoncanonical | |
| Ccore::scoring::methods::SequenceDependentRefEnergy | |
| Ccore::scoring::methods::SymmetricLigandEnergy | |
| Ccore::scoring::methods::UnfoldedStateEnergy | |
| Ccore::scoring::methods::WaterAdductIntraEnergy | |
| Ccore::scoring::methods::YHHPlanarityEnergy | |
| Ccore::scoring::rna::RNA_BulgeEnergy | |
| Ccore::scoring::rna::RNA_FullAtomVDW_BasePhosphate | |
| Ccore::scoring::rna::RNA_SugarCloseEnergy | |
| ►Ccore::scoring::methods::TwoBodyEnergy | |
| ►Ccore::scoring::methods::LongRangeTwoBodyEnergy | |
| ►Ccore::scoring::methods::ContextDependentLRTwoBodyEnergy | |
| Ccore::scoring::electron_density::ElecDensAllAtomCenEnergy | |
| Ccore::scoring::electron_density::ElecDensCenEnergy | |
| Ccore::scoring::electron_density::PattersonCorrEnergy | |
| Ccore::scoring::methods::GenBornEnergy | |
| Ccore::scoring::sym_e::symEnergy | |
| ►Ccore::scoring::methods::ContextIndependentLRTwoBodyEnergy | |
| Ccore::scoring::constraints::ConstraintsEnergy | |
| Ccore::scoring::disulfides::CentroidDisulfideEnergy | |
| Ccore::scoring::disulfides::DisulfideMatchingEnergy | |
| Ccore::scoring::disulfides::FullatomDisulfideEnergy | |
| Ccore::scoring::electron_density::ElecDensEnergy | |
| Ccore::scoring::electron_density::FastDensEnergy | |
| Ccore::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy | |
| Ccore::scoring::methods::CartesianBondedEnergy | |
| Ccore::scoring::methods::dfire::DFIRE_Energy | |
| Ccore::scoring::methods::PoissonBoltzmannEnergy | |
| Ccore::scoring::methods::Rama2BOffsetEnergy | |
| Ccore::scoring::rna::RNA_SuiteEnergy | |
| ►Ccore::scoring::methods::ShortRangeTwoBodyEnergy | |
| ►Ccore::scoring::methods::ContextDependentTwoBodyEnergy | |
| Ccore::scoring::elec::FA_GrpElecEnergy | |
| Ccore::scoring::geometric_solvation::ContextDependentGeometricSolEnergy | |
| Ccore::scoring::hbonds::HBondEnergy | |
| Ccore::scoring::interface_::DDPscore | |
| Ccore::scoring::membrane::FaMPSolvEnergy | Energy Method: Membrane Fullaotm Solvation Energy (LK) |
| Ccore::scoring::membrane::MPPairEnergy | Membrane Environemtn Residue Pair Energy Term |
| Ccore::scoring::methods::Fa_MbsolvEnergy | |
| Ccore::scoring::methods::FACTSEnergy | |
| Ccore::scoring::methods::MembraneCenPairEnergy | |
| Ccore::scoring::methods::PairEnergy | |
| Ccore::scoring::orbitals::OrbitalsScore | |
| Ccore::scoring::rna::RNA_FullAtomStackingEnergy | |
| ►Ccore::scoring::methods::ContextIndependentTwoBodyEnergy | |
| ►Ccore::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy > | |
| Ccore::scoring::etable::AnalyticEtableEnergy | |
| Ccore::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy > | |
| Ccore::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy > | |
| ►Ccore::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy > | |
| Ccore::scoring::etable::CoarseEtableEnergy | |
| Ccore::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy > | |
| Ccore::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy > | |
| ►Ccore::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy > | |
| Ccore::scoring::etable::TableLookupEtableEnergy | |
| Ccore::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy > | |
| Ccore::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy > | |
| Ccore::scoring::carbon_hbonds::CarbonHBondEnergy | |
| Ccore::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy | |
| Ccore::scoring::dna::DNATorsionEnergy | |
| ►Ccore::scoring::elec::FA_ElecEnergy | |
| Ccore::scoring::elec::FA_ElecEnergyAroAll | |
| Ccore::scoring::elec::FA_ElecEnergyAroAro | |
| Ccore::scoring::elec::RNA_FA_ElecEnergy | |
| Ccore::scoring::etable::BaseEtableEnergy< Derived > | |
| Ccore::scoring::etable::BaseEtableEnergy< Derived > | |
| Ccore::scoring::etable::BaseEtableEnergy< Derived > | |
| Ccore::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy | |
| Ccore::scoring::geometric_solvation::OccludedHbondSolEnergy | |
| Ccore::scoring::hackaro::HackAroEnergy | |
| Ccore::scoring::methods::CenHBEnergy | |
| Ccore::scoring::methods::CenPairEnergy | |
| Ccore::scoring::methods::CenRotPairEnergy | |
| Ccore::scoring::methods::CSD_TorsionEnergy | A knowledge-based torsional potential for small molecules derived from the Cambridge Structural Database by KWK |
| Ccore::scoring::methods::CustomAtomPairEnergy | |
| Ccore::scoring::methods::DNA_BaseEnergy | |
| Ccore::scoring::methods::GaussianOverlapEnergy | |
| Ccore::scoring::methods::GoapEnergy | |
| Ccore::scoring::methods::HybridVDW_Energy | |
| Ccore::scoring::methods::LK_BallEnergy | |
| Ccore::scoring::methods::LK_hack | |
| Ccore::scoring::methods::LK_PolarNonPolarEnergy | |
| Ccore::scoring::methods::MMBondAngleEnergy | |
| Ccore::scoring::methods::MMBondLengthEnergy | |
| Ccore::scoring::methods::MMLJEnergyInter | |
| Ccore::scoring::methods::MMLJEnergyIntra | |
| Ccore::scoring::methods::MMTorsionEnergy | |
| Ccore::scoring::methods::PeptideBondEnergy | PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment |
| Ccore::scoring::methods::ProClosureEnergy | |
| Ccore::scoring::methods::RamachandranEnergy2B | |
| Ccore::scoring::methods::SmoothCenPairEnergy | |
| Ccore::scoring::methods::SuckerEnergy | |
| Ccore::scoring::methods::WaterAdductHBondEnergy | |
| Ccore::scoring::rna::data::RNA_DataBackboneEnergy | |
| Ccore::scoring::rna::RNA_JR_SuiteEnergy | |
| Ccore::scoring::rna::RNA_LJ_BaseEnergy | |
| Ccore::scoring::rna::RNA_Mg_Energy | |
| Ccore::scoring::rna::RNA_PairwiseLowResolutionEnergy | |
| Ccore::scoring::rna::RNA_TorsionEnergy | |
| Ccore::scoring::rna::RNA_VDW_Energy | |
| Ccore::scoring::rna::StackElecEnergy | |
| Ccore::scoring::vdwaals::VDW_Energy | |
| Ccore::scoring::vdwaals::VDW_Energy | |
| ►Ccore::scoring::methods::WholeStructureEnergy | Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation |
| Ccore::scoring::cryst::XtalMLEnergy | |
| Ccore::scoring::loop_graph::LoopCloseEnergy | |
| Ccore::scoring::membrane::MPLipoEnergy | Membrane Lipophilicity term |
| Ccore::scoring::membrane::MPTMProjPenalty | Class Membrane TM proj Penalty |
| Ccore::scoring::methods::ChainbreakEnergy | ChainbreakEnergy class iterates across all residues in finalize() and determines a penalty between residues i and i+1 across a cutpoint by how much their virtual atoms do not align |
| Ccore::scoring::methods::ChemicalShiftAnisotropyEnergy | |
| Ccore::scoring::methods::ContactOrderEnergy | |
| Ccore::scoring::methods::D2H_SA_Energy | |
| Ccore::scoring::methods::DipolarCouplingEnergy | |
| Ccore::scoring::methods::DirectReadoutEnergy | Implementation of Kono and Sarai's knowledge-based protein-DNA interaction energy |
| Ccore::scoring::methods::DistanceChainbreakEnergy | DistanceChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how far apart their N and C atom are |
| Ccore::scoring::methods::IntermolEnergy | |
| Ccore::scoring::methods::LinearChainbreakEnergy | LinearChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align |
| Ccore::scoring::methods::MembraneEnvPenalties | |
| Ccore::scoring::methods::MembraneLipo | |
| Ccore::scoring::methods::MetalloPlacementEnergy | |
| Ccore::scoring::methods::MissingEnergy | |
| Ccore::scoring::methods::OtherPoseEnergy | |
| Ccore::scoring::methods::PackStatEnergy | |
| Ccore::scoring::methods::ProQ_Energy | |
| Ccore::scoring::methods::ResidualDipolarCouplingEnergy | |
| Ccore::scoring::methods::ResidualDipolarCouplingEnergy_Rohl | |
| Ccore::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments | |
| Ccore::scoring::methods::RG_Energy | |
| ►Ccore::scoring::methods::RG_Energy_Fast | |
| Ccore::scoring::methods::RG_LocalEnergy | |
| Ccore::scoring::methods::RMS_Energy | |
| Ccore::scoring::methods::SA_Energy | |
| Ccore::scoring::methods::SecondaryStructureEnergy | |
| Ccore::scoring::packing::HolesEnergy | |
| Ccore::scoring::packing::HolesEnergyRes | |
| Ccore::scoring::packing::SurfEnergy | |
| Ccore::scoring::packing::SurfVolEnergy | |
| Ccore::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy | |
| Ccore::scoring::rna::data::RNA_ChemicalMappingEnergy | |
| Ccore::scoring::rna::RG_Energy_RNA | |
| Ccore::scoring::rna::RNA_BaseBaseEnergy | |
| Ccore::scoring::saxs::FastSAXSEnergy | |
| ►Ccore::scoring::saxs::SAXSEnergy | |
| Ccore::scoring::saxs::SAXSEnergyCEN | |
| Ccore::scoring::saxs::SAXSEnergyFA | |
| ►Ccore::scoring::methods::EnergyMethodCreator | The EnergyMethodCreator class's responsibilities are to create on demand a new EnergyMethod class, and to tell the ScoringManager singleton which ScoreTypes the EnergyMethod it creates is responsible for. The EnergyMethodCreator must register itself with the ScoringManager at load time (before main() begins) so that the ScoringManager is ready to start creating EnergyMethods by the time the first ScoreFunction requests one |
| Ccore::pack::dunbrack::cenrot::CenRotDunEnergyCreator | |
| Ccore::pack::dunbrack::DunbrackEnergyCreator | |
| Ccore::pack::interaction_graph::HPatchEnergyCreator | |
| Ccore::pack::interaction_graph::SurfaceEnergyCreator | |
| Ccore::scoring::carbon_hbonds::CarbonHBondEnergyCreator | |
| Ccore::scoring::constraints::ConstraintsEnergyCreator | |
| Ccore::scoring::cryst::XtalMLEnergyCreator | |
| Ccore::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator | |
| Ccore::scoring::disulfides::CentroidDisulfideEnergyCreator | |
| Ccore::scoring::disulfides::DisulfideMatchingEnergyCreator | |
| Ccore::scoring::disulfides::FullatomDisulfideEnergyCreator | |
| Ccore::scoring::dna::DNAChiEnergyCreator | |
| Ccore::scoring::dna::DNATorsionEnergyCreator | |
| Ccore::scoring::elec::FA_ElecEnergyAroAllCreator | |
| Ccore::scoring::elec::FA_ElecEnergyAroAroCreator | |
| Ccore::scoring::elec::FA_ElecEnergyCreator | |
| Ccore::scoring::elec::FA_GrpElecEnergyCreator | |
| Ccore::scoring::elec::RNA_FA_ElecEnergyCreator | |
| Ccore::scoring::electron_density::ElecDensAllAtomCenEnergyCreator | |
| Ccore::scoring::electron_density::ElecDensCenEnergyCreator | |
| Ccore::scoring::electron_density::ElecDensEnergyCreator | |
| Ccore::scoring::electron_density::FastDensEnergyCreator | |
| Ccore::scoring::electron_density::PattersonCorrEnergyCreator | |
| Ccore::scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator | |
| Ccore::scoring::etable::CoarseEtableEnergyCreator | |
| Ccore::scoring::etable::EtableClassicIntraEnergyCreator | |
| Ccore::scoring::etable::EtableEnergyCreator | |
| Ccore::scoring::geometric_solvation::ContextDependentGeometricSolEnergyCreator | |
| Ccore::scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator | |
| Ccore::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator | |
| Ccore::scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator | |
| Ccore::scoring::geometric_solvation::OccludedHbondSolEnergyCreator | |
| Ccore::scoring::hackaro::HackAroEnergyCreator | |
| Ccore::scoring::hbonds::HBondEnergyCreator | |
| Ccore::scoring::interface_::DDPscoreCreator | |
| Ccore::scoring::loop_graph::LoopCloseEnergyCreator | |
| Ccore::scoring::membrane::FaMPEnvEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| Ccore::scoring::membrane::FaMPEnvSmoothEnergyCreator | Membrane Termini Penalty Creator Class |
| Ccore::scoring::membrane::FaMPSolvEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| Ccore::scoring::membrane::MPCbetaEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| Ccore::scoring::membrane::MPEnvEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| Ccore::scoring::membrane::MPLipoEnergyCreator | Creator Class for MPLipoEnergy |
| Ccore::scoring::membrane::MPNonHelixPenaltyCreator | Membrane Non Hleix in mmebrane Penalty Creator Class |
| Ccore::scoring::membrane::MPPairEnergyCreator | Creator Class for Membrane Residue Pair Energy Method |
| Ccore::scoring::membrane::MPTerminiPenaltyCreator | Membrane Termini Penalty Creator Class |
| Ccore::scoring::membrane::MPTMProjPenaltyCreator | Membrane TM Proj Penalty Creator Class |
| Ccore::scoring::methods::BurialEnergyCreator | |
| Ccore::scoring::methods::CartesianBondedEnergyCreator | |
| Ccore::scoring::methods::CenHBEnergyCreator | |
| Ccore::scoring::methods::CenPairEnergyCreator | |
| Ccore::scoring::methods::CenRotEnvEnergyCreator | |
| Ccore::scoring::methods::CenRotPairEnergyCreator | |
| Ccore::scoring::methods::ChainbreakEnergyCreator | |
| Ccore::scoring::methods::ChemicalShiftAnisotropyEnergyCreator | |
| Ccore::scoring::methods::ContactOrderEnergyCreator | |
| Ccore::scoring::methods::CustomAtomPairEnergyCreator | |
| Ccore::scoring::methods::D2H_SA_EnergyCreator | |
| Ccore::scoring::methods::dfire::DFIRE_EnergyCreator | |
| Ccore::scoring::methods::DipolarCouplingEnergyCreator | |
| Ccore::scoring::methods::DirectReadoutEnergyCreator | |
| Ccore::scoring::methods::DistanceChainbreakEnergyCreator | |
| Ccore::scoring::methods::DNA_BaseEnergyCreator | |
| Ccore::scoring::methods::EnvEnergyCreator | |
| Ccore::scoring::methods::EnvSmoothEnergyCreator | |
| Ccore::scoring::methods::Fa_MbenvEnergyCreator | |
| Ccore::scoring::methods::Fa_MbsolvEnergyCreator | |
| Ccore::scoring::methods::FACTSEnergyCreator | |
| Ccore::scoring::methods::FreeDOF_EnergyCreator | |
| Ccore::scoring::methods::GaussianOverlapEnergyCreator | |
| Ccore::scoring::methods::GenBornEnergyCreator | |
| Ccore::scoring::methods::GoapEnergyCreator | |
| Ccore::scoring::methods::HybridVDW_EnergyCreator | |
| Ccore::scoring::methods::IntermolEnergyCreator | |
| Ccore::scoring::methods::LinearChainbreakEnergyCreator | |
| Ccore::scoring::methods::LK_BallEnergyCreator | |
| Ccore::scoring::methods::LK_hackCreator | |
| Ccore::scoring::methods::LK_PolarNonPolarEnergyCreator | |
| Ccore::scoring::methods::MembraneCbetaEnergyCreator | |
| Ccore::scoring::methods::MembraneCenPairEnergyCreator | |
| Ccore::scoring::methods::MembraneEnvEnergyCreator | |
| Ccore::scoring::methods::MembraneEnvPenaltiesCreator | |
| Ccore::scoring::methods::MembraneEnvSmoothEnergyCreator | |
| Ccore::scoring::methods::MembraneLipoCreator | |
| Ccore::scoring::methods::MissingEnergyCreator | |
| Ccore::scoring::methods::MMBondAngleEnergyCreator | |
| Ccore::scoring::methods::MMBondLengthEnergyCreator | |
| Ccore::scoring::methods::MMLJEnergyInterCreator | |
| Ccore::scoring::methods::MMLJEnergyIntraCreator | |
| Ccore::scoring::methods::MMTorsionEnergyCreator | |
| Ccore::scoring::methods::NMerPSSMEnergyCreator | |
| Ccore::scoring::methods::NMerRefEnergyCreator | |
| Ccore::scoring::methods::NMerSVMEnergyCreator | |
| Ccore::scoring::methods::OmegaTetherEnergyCreator | |
| Ccore::scoring::methods::OtherPoseEnergyCreator | |
| Ccore::scoring::methods::P_AA_EnergyCreator | |
| Ccore::scoring::methods::P_AA_pp_EnergyCreator | |
| Ccore::scoring::methods::PackStatEnergyCreator | |
| Ccore::scoring::methods::PairEnergyCreator | |
| Ccore::scoring::methods::PeptideBondEnergyCreator | |
| Ccore::scoring::methods::pHEnergyCreator | |
| Ccore::scoring::methods::PoissonBoltzmannEnergyCreator | |
| Ccore::scoring::methods::ProClosureEnergyCreator | |
| Ccore::scoring::methods::ProQ_EnergyCreator | |
| Ccore::scoring::methods::Rama2BOffsetEnergyCreator | |
| Ccore::scoring::methods::RamachandranEnergy2BCreator | |
| Ccore::scoring::methods::RamachandranEnergyCreator | |
| Ccore::scoring::methods::ReferenceEnergyCreator | |
| Ccore::scoring::methods::ReferenceEnergyNoncanonicalCreator | |
| Ccore::scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator | |
| Ccore::scoring::methods::ResidualDipolarCouplingEnergyCreator | |
| Ccore::scoring::methods::RG_Energy_FastCreator | |
| Ccore::scoring::methods::RG_LocalEnergyCreator | |
| Ccore::scoring::methods::RMS_EnergyCreator | |
| Ccore::scoring::methods::SA_EnergyCreator | |
| Ccore::scoring::methods::SecondaryStructureEnergyCreator | |
| Ccore::scoring::methods::SequenceDependentRefEnergyCreator | |
| Ccore::scoring::methods::SmoothCenPairEnergyCreator | |
| Ccore::scoring::methods::SmoothEnvEnergyCreator | |
| Ccore::scoring::methods::SuckerEnergyCreator | |
| Ccore::scoring::methods::SymmetricLigandEnergyCreator | |
| Ccore::scoring::methods::UnfoldedStateEnergyCreator | |
| Ccore::scoring::methods::WaterAdductHBondEnergyCreator | |
| Ccore::scoring::methods::WaterAdductIntraEnergyCreator | |
| Ccore::scoring::methods::YHHPlanarityEnergyCreator | |
| Ccore::scoring::nv::NVscoreCreator | |
| Ccore::scoring::orbitals::OrbitalsScoreCreator | |
| Ccore::scoring::packing::HolesEnergyCreator | |
| Ccore::scoring::packing::SurfEnergyCreator | |
| Ccore::scoring::packing::SurfVolEnergyCreator | |
| Ccore::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergyCreator | |
| Ccore::scoring::rna::data::RNA_ChemicalMappingEnergyCreator | |
| Ccore::scoring::rna::data::RNA_DataBackboneEnergyCreator | |
| Ccore::scoring::rna::RG_Energy_RNACreator | |
| Ccore::scoring::rna::RNA_BulgeEnergyCreator | |
| Ccore::scoring::rna::RNA_FullAtomStackingEnergyCreator | |
| Ccore::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator | |
| Ccore::scoring::rna::RNA_JR_SuiteEnergyCreator | |
| Ccore::scoring::rna::RNA_LJ_BaseEnergyCreator | |
| Ccore::scoring::rna::RNA_Mg_EnergyCreator | |
| Ccore::scoring::rna::RNA_PairwiseLowResolutionEnergyCreator | |
| Ccore::scoring::rna::RNA_SugarCloseEnergyCreator | |
| Ccore::scoring::rna::RNA_SuiteEnergyCreator | |
| Ccore::scoring::rna::RNA_TorsionEnergyCreator | |
| Ccore::scoring::rna::RNA_VDW_EnergyCreator | |
| Ccore::scoring::rna::StackElecEnergyCreator | |
| Ccore::scoring::saxs::FastSAXSEnergyCreator | |
| ►Ccore::scoring::saxs::SAXSEnergyCreator | |
| Ccore::scoring::saxs::SAXSEnergyCreatorCEN | |
| Ccore::scoring::saxs::SAXSEnergyCreatorFA | |
| Ccore::scoring::sym_e::symECreator | |
| Ccore::scoring::vdwaals::VDW_EnergyCreator | |
| Ccore::scoring::methods::EnergyMethodOptions | |
| Ccore::scoring::methods::FreeDOF_Options | |
| Ccore::scoring::methods::GoapRsdType | |
| Ccore::scoring::methods::IdealParametersDatabase | |
| Ccore::scoring::methods::ResidueCartBondedParameters | |
| Ccore::scoring::mm::MMBondAngleLibrary | |
| Ccore::scoring::mm::MMBondAngleResidueTypeParamSet | |
| Ccore::scoring::mm::MMBondAngleScore | Calculates scores of mm bond angle paramater sets given an angle |
| Ccore::scoring::mm::MMBondLengthLibrary | |
| Ccore::scoring::mm::MMBondLengthScore | |
| Ccore::scoring::mm::MMLJEnergyTable | Blah |
| Ccore::scoring::mm::MMLJLibrary | A class to maintain a set of MM LJ paramaters |
| Ccore::scoring::mm::MMLJScore | Calculates scores of mm lj paramater sets given two mm atom types, the path distance of the 2 atoms and actual distance between the two atoms |
| Ccore::scoring::mm::MMTorsionLibrary | A class to maintain a set of MM torsion paramaters |
| Ccore::scoring::mm::MMTorsionScore | Calculates scores of mm torsion paramater sets given an angle |
| Ccore::scoring::motif::MotifHash | |
| Ccore::scoring::motif::XformScore | |
| Ccore::scoring::motif::XfragSet | |
| Ccore::scoring::NeighborList | |
| Ccore::scoring::nv::NVlookup | |
| Ccore::scoring::OmegaTether | |
| Ccore::scoring::orbitals::OrbitalsLookup | |
| Ccore::scoring::P_AA | |
| Ccore::scoring::packing::Ball | |
| Ccore::scoring::packing::HolesResult | Result class holding the three scores and the per-atom scores |
| Ccore::scoring::packing::PoseBalls | |
| Ccore::scoring::packing::PoseBallsLite | |
| ►Ccore::scoring::packstat::Accumulator | |
| Ccore::scoring::packstat::AreaAccumulator | |
| Ccore::scoring::packstat::MultiProbePerSphereAccumulator | |
| Ccore::scoring::packstat::MultiProbePoseAccumulator | |
| Ccore::scoring::packstat::PerSphereAccumulator | |
| Ccore::scoring::packstat::PackingScore | |
| Ccore::scoring::packstat::PackingScoreResData | |
| Ccore::scoring::packstat::PosePackData | |
| Ccore::scoring::packstat::SasaOptions | |
| Ccore::scoring::packstat::SasaResult | |
| Ccore::scoring::PairEPotential | |
| Ccore::scoring::PoissonBoltzmannPotential | |
| Ccore::scoring::PQR | |
| ►Ccore::scoring::Predicate | |
| Ccore::scoring::ExcludedResPredicate | |
| Ccore::scoring::IsProteinCAPredicate | |
| Ccore::scoring::ResRangePredicate | |
| Ccore::scoring::SelectedResPredicate | |
| Ccore::scoring::Rama2BOffset | |
| Ccore::scoring::Ramachandran | |
| Ccore::scoring::Ramachandran2B | |
| ►Ccore::scoring::ResidueNeighborConstIterator | |
| Ccore::scoring::constraints::CstResNeighbConstIterator | |
| Ccore::scoring::DenseNeighborConstIterator | |
| Ccore::scoring::disulfides::CentroidDisulfideNeighborConstIterator | Just a const version of CentroidDisulfideNeighborIterator |
| Ccore::scoring::disulfides::DisulfideMatchingNeighborConstIterator | Just a const version of DisulfideMatchingNeighborIterator |
| Ccore::scoring::disulfides::DisulfResNeighbConstIterator | |
| Ccore::scoring::OneToAllNeighborConstIterator | |
| Ccore::scoring::PeptideBondedNeighborConstIterator | |
| ►Ccore::scoring::ResidueNeighborIterator | |
| Ccore::scoring::constraints::CstResNeighbIterator | |
| Ccore::scoring::DenseNeighborIterator | |
| Ccore::scoring::disulfides::CentroidDisulfideNeighborIterator | An iterator over the disulfide bonds a residue forms |
| Ccore::scoring::disulfides::DisulfideMatchingNeighborIterator | An iterator over the disulfide bonds a residue forms |
| Ccore::scoring::disulfides::DisulfResNeighbIterator | |
| Ccore::scoring::OneToAllNeighborIterator | |
| Ccore::scoring::PeptideBondedNeighborIterator | |
| Ccore::scoring::ResPairMinimizationData | |
| Ccore::scoring::ResSingleMinimizationData | |
| Ccore::scoring::rna::chemical_shift::ChemicalShiftData | |
| Ccore::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential | |
| Ccore::scoring::rna::chemical_shift::RNA_CS_parameters | |
| Ccore::scoring::rna::chemical_shift::RNA_CS_residue_parameters | |
| Ccore::scoring::rna::data::RNA_DataInfo | Keep track of RNA chemical mapping data inside the pose |
| Ccore::scoring::rna::data::RNA_DMS_LowResolutionPotential | |
| Ccore::scoring::rna::data::RNA_DMS_Potential | |
| Ccore::scoring::rna::RNA_AtomVDW | |
| Ccore::scoring::rna::RNA_EnergyMethodOptions | |
| Ccore::scoring::rna::RNA_LowResolutionPotential | |
| Ccore::scoring::rna::RNA_Mg_KnowledgeBasedPotential | |
| Ccore::scoring::rna::RNA_SuitePotential | |
| Ccore::scoring::rna::RNA_TorsionPotential | |
| Ccore::scoring::RsdEnergiesBreakdown | |
| Ccore::scoring::sasa::SasaCalc | Main interface to sasa calculations outside of pose metrics |
| ►Ccore::scoring::sasa::SasaMethod | Abstract base class for SasaMethods. Feel free to edit as needed |
| Ccore::scoring::sasa::LeGrandSasa | LeGrand SASA approximation method Used by SasaCalc but can be used by itself |
| Ccore::scoring::saxs::DistanceHistogram | |
| Ccore::scoring::saxs::FormFactor | |
| ►Ccore::scoring::sc::MolecularSurfaceCalculator | |
| Ccore::scoring::sc::ShapeComplementarityCalculator | |
| Ccore::scoring::ScoreFunction | This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated |
| Ccore::scoring::ScoreFunctionInfo | Info on the scorefunction settings |
| Ccore::scoring::SecondaryStructurePotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| Ccore::scoring::SecondaryStructureWeights | Holds weights and flags for configuring a SecondaryStructureEnergy evaluation |
| Ccore::scoring::SmoothEnvPairPotential | |
| ►Ccore::scoring::trie::TrieCountPairBase | |
| Ccore::scoring::etable::etrie::TrieCountPair1BC3 | |
| Ccore::scoring::etable::etrie::TrieCountPair1BC4 | |
| Ccore::scoring::etable::etrie::TrieCountPairAll | |
| Ccore::scoring::etable::etrie::TrieCountPairGeneric | |
| Ccore::scoring::etable::etrie::TrieCountPairNone | |
| Ccore::scoring::hbonds::hbtrie::HBCountPairFunction | |
| Ccore::scoring::vdwaals::VDWTrieCountPair1B | |
| Ccore::scoring::UnfoldedStatePotential | |
| Ccore::scoring::WaterAdductHBondPotential | |
| ►Ccore::sequence::Aligner | |
| Ccore::sequence::ExtendAlignerSW | |
| Ccore::sequence::MCAligner | |
| Ccore::sequence::NWAligner | |
| Ccore::sequence::SWAligner | |
| Ccore::sequence::Cell | |
| Ccore::sequence::DP_Matrix | |
| ►Ccore::sequence::ScoringScheme | |
| Ccore::sequence::ChemicalShiftScoringScheme | |
| Ccore::sequence::CompassScoringScheme | |
| Ccore::sequence::CompositeScoringScheme | |
| Ccore::sequence::DPScoringScheme | |
| Ccore::sequence::L1ScoringScheme | |
| Ccore::sequence::MatrixScoringScheme | |
| Ccore::sequence::PairScoringScheme | |
| Ccore::sequence::ProfSimScoringScheme | |
| Ccore::sequence::SimpleScoringScheme | |
| ►Ccore::sequence::Sequence | |
| Ccore::sequence::CompositeSequence | |
| ►Ccore::sequence::SequenceProfile | |
| Ccore::sequence::ChemicalShiftSequence | |
| Ccore::sequence::SequenceCoupling | |
| Ccore::sequence::SequenceAlignment | |
| ►Ccore::sequence::SequenceCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| Ccore::sequence::ChemicalShiftSequenceCreator | |
| Ccore::sequence::CompositeSequenceCreator | |
| Ccore::sequence::SequenceCouplingCreator | |
| Ccore::sequence::SequenceProfileCreator | |
| Ccore::sequence::SimpleSequenceCreator | |
| Ccore::util::ABEGOManager | Manager for abego |
| Ccore::graph::UpperEdgeGraph< Vertex, Edge > | |
| Ccore::pose::RemarkInfo | |
| Ccore::chemical::RerootEdgeSorter | Edge sorting: Return true if we should prefer edge1 over edge2 |
| Ccore::scoring::custom_pair_distance::resatom_and_func_struct | |
| Ccore::chemical::ResConnID | The 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 |
| Ccore::pack::task::operation::ResFilterFactory | |
| Ccore::chemical::ResidueConnection | A simple class marking atoms at inter-residue connections |
| Ccore::conformation::ResidueFactory | Collection of functions making a single residue |
| Ccore::io::pdb::ResidueInformation | Intermediate format for easy construction of core::conformation::Residue objects |
| Ccore::pose::PDBPoseMap::ResidueKey | Sortable residue key internal to PDBPoseMap |
| ►Ccore::pack::task::ResidueLevelTask | |
| Ccore::pack::task::ResidueLevelTask_ | Residue-level task class; contained within PackerTask |
| Ccore::pose::PDBInfo::ResidueRecord | Internal struct for storing PDB residue related information |
| Ccore::pack::task::residue_selector::ResidueSelectorFactory | |
| Ccore::io::raw_data::DisulfideFile::ResNum | Residue of either pdb or rosetta numbering |
| ►Cbasic::resource_manager::ResourceLoader [external] | |
| Ccore::chemical::ResidueLoader | |
| Ccore::conformation::symmetry::SymmDataLoader | |
| Ccore::import_pose::PoseFromPDBLoader | |
| Ccore::io::silent::SilentFileLoader | |
| Ccore::scoring::electron_density::ElectronDensityLoader | |
| ►Cbasic::resource_manager::ResourceLoaderCreator [external] | |
| Ccore::chemical::ResidueLoaderCreator | |
| Ccore::conformation::symmetry::SymmDataLoaderCreator | |
| Ccore::import_pose::PoseFromPDBLoaderCreator | |
| Ccore::io::silent::SilentFileLoaderCreator | Creator for the SilentFileLoader class |
| Ccore::scoring::electron_density::ElectronDensityLoaderCreator | Creator for the ElectronDensityLoader class |
| ►Cbasic::resource_manager::ResourceOptions [external] | |
| Ccore::chemical::ResidueLoaderOptions | |
| Ccore::conformation::symmetry::SymmDataOptions | |
| ►Ccore::io::pdb::FileDataOptions | |
| ►Ccore::io::pdb::PDB_DReaderOptions | |
| Ccore::import_pose::ImportPoseOptions | This class contains all of the data which is used in the process of reading a PDB into a Pose. There is actually a substantial amount of data! |
| Ccore::io::silent::SilentFileOptions | |
| Ccore::scoring::electron_density::ElectronDensityOptions | |
| ►Cbasic::resource_manager::ResourceOptionsCreator [external] | |
| Ccore::chemical::ResidueLoaderOptionsCreator | |
| Ccore::conformation::symmetry::SymmDataOptionsCreator | |
| Ccore::import_pose::ImportPoseOptionsCreator | |
| Ccore::io::silent::SilentFileOptionsCreator | Creator for the SilentFileOptions class |
| Ccore::scoring::electron_density::ElectronDensityOptionsCreator | Creator for the ElectronDensityOptions class |
| Ccore::scoring::motif::ResPairMotif | |
| Ccore::scoring::motif::ResPairMotifMetaBinner | |
| Ccore::scoring::motif::ResPairMotifQuery | |
| Ccore::chemical::RingConformer | |
| Ccore::scoring::motif::RMSandEnergyCMP | |
| Ccore::scoring::rna::data::RNA_Datum | |
| Ccore::scoring::rna::data::RNA_Reactivity | |
| Ccore::pose::rna::RNA_SuiteAssignment | |
| Ccore::pose::rna::RNA_SuiteInfo | |
| Ccore::scoring::trie::RotamerDescriptor< AT, CPDAT > | |
| Ccore::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > | |
| Ccore::pack::interaction_graph::RotamerDotsCache | A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes |
| Ccore::pack::annealer::RotSub | |
| Ccore::scoring::motif::RPM_FilterStats | |
| Ccore::kinematics::RT | Rotation + translation class |
| Ccore::scoring::disulfides::RT_helper | |
| Ccore::pack::RTMin | |
| Ccore::scoring::ScoreFunctionFactory | Collection of functions making a single score_function |
| Ccore::import_pose::atom_tree_diffs::ScoreLessThanComparator | Provides a StrictWeakOrdering comparator for sorting elements of a ScoresMap by one particular score type |
| Ccore::scoring::ScoreTypeManager | |
| Ccore::sequence::ScoringSchemeFactory | |
| Ccore::chemical::sdf::SDFParser | |
| ►Cutility::Show [external] | |
| Ccore::io::pdb::Field | Data type Class to represent one field in PDB file |
| Ccore::io::silent::SilentEnergy | Helper class for silent-file classes to keep track of energy information |
| Ccore::scoring::packstat::SimplePDB | |
| Ccore::scoring::packstat::SimplePDB_Atom | |
| Ccore::pack::dunbrack::SingleResidueDunbrackLibraryConcrete< T > | |
| ►Cutility::SingletonBase< ChemicalManager > [external] | |
| Ccore::chemical::ChemicalManager | Class managing different sets of atom_type_set and residue_type_set |
| ►Cutility::SingletonBase< ConstraintFactory > [external] | |
| Ccore::scoring::constraints::ConstraintFactory | |
| ►Cutility::SingletonBase< ConstraintIO > [external] | |
| Ccore::scoring::constraints::ConstraintIO | |
| ►Cutility::SingletonBase< FragmentLibraryManager > [external] | |
| Ccore::fragment::picking_old::FragmentLibraryManager | Singleton class for accessing fragment libraries |
| ►Cutility::SingletonBase< GridInfo > [external] | |
| Ccore::scoring::geometric_solvation::GridInfo | |
| ►Cutility::SingletonBase< ResLvlTaskOperationFactory > [external] | |
| Ccore::pack::task::operation::ResLvlTaskOperationFactory | |
| ►Cutility::SingletonBase< RotamerDotsRadiusData > [external] | |
| Ccore::pack::interaction_graph::RotamerDotsRadiusData | A singleton class which reads in database SASA radii files and provides accessors for those values to the RotamerDots class |
| ►Cutility::SingletonBase< RotamerLibrary > [external] | |
| Ccore::pack::dunbrack::RotamerLibrary | |
| ►Cutility::SingletonBase< ScoringManager > [external] | |
| Ccore::scoring::ScoringManager | |
| ►Cutility::SingletonBase< SequenceFactory > [external] | |
| Ccore::sequence::SequenceFactory | |
| ►Cutility::SingletonBase< SilentStructFactory > [external] | |
| Ccore::io::silent::SilentStructFactory | |
| ►Cutility::SingletonBase< SinXOverX > [external] | |
| Ccore::scoring::saxs::SinXOverX | |
| ►Cutility::SingletonBase< StructureStoreManager > [external] | |
| Ccore::indexed_structure_store::StructureStoreManager | |
| ►Cutility::SingletonBase< SurfacePotential > [external] | |
| Ccore::pack::interaction_graph::SurfacePotential | With the traditional scoring hierarchy, classes like this one are created and accessed via the ScoringManager, which is itself a Singleton class. These "potential" classes are only created and initialized when the use of the EnergyMethod these classes correspond is encountered. No point in reading database files for a term if that term is not being used in some score function. However, the surface energy is used when users specify they want to use it on the command line - NOT via a score function. The score/energy is done within an interaction graph. One might ask why I just don't put the logic for reading in the database file to the interaction graph init methods. However, there will be cases where I will want to just score a protein (and not do any design) where I will want the database file to be read in. Scoring doesn't use interaction graphs, so if the code for that was located there, these values would not be read in. Instead, I've decided to implement this as its own separate class. It uses the Singleton design pattern so the database will only get read in once during a run |
| ►Cutility::SingletonBase< WaterWeightGridSet > [external] | |
| Ccore::scoring::geometric_solvation::WaterWeightGridSet | |
| Ccore::scoring::packstat::Slice | |
| Ccore::scoring::SmallAtNb | |
| Ccore::scoring::SmoothScoreTermCoeffs | |
| Ccore::optimization::sort_pred | |
| Ccore::pack::interaction_graph::SparseMatrixIndex | |
| Ccore::scoring::packstat::Sphere | |
| Ccore::scoring::etable::SplineParameters | SplineParameters is a simple struct for holding the cubic spline polynomials used in the etable to interpolate the lennard-jones attractive and LK-solvation terms to zero smoothly. These splines have exactly two knots to represent them, and the same x values are used for all the knots: thus the only parameters needed are the y values at the knots, and the second-derivatives for the polynomials at knots |
| Ccore::scoring::hbonds::SSWeightParameters | |
| Ccore::scoring::dssp::StrandPairing | |
| Ccore::scoring::Strands | |
| Ccore::kinematics::Stub | Stub class – an object of orthogonal coordinate frame |
| Ccore::id::StubID | |
| Ccore::scoring::packing::SurfVol | |
| Ccore::scoring::packing::SurfVolDeriv | |
| Ccore::SVNVersion | |
| Ccore::conformation::symmetry::SymDof | |
| Ccore::conformation::symmetry::SymmDataFactory | |
| Ccore::conformation::symmetry::SymSlideInfo | |
| Ccore::pack::task::operation::TaskOperationFactory | |
| Ccore::scoring::TMscore | |
| Ccore::scoring::TMscoreStore | |
| Ccore::id::TorsionID | Torsion identifier class |
| Ccore::id::TorsionID_Range | Kinematics DOF identifier (with range) class |
| Ccore::scoring::packstat::trace | |
| Ccore::kinematics::TreeVizBuilder | |
| Ccore::scoring::trie::TrieNode< AT, CPDATA > | |
| Ccore::graph::UEEdge< V, E > | |
| ►Cunary_function | |
| Ccore::conformation::DefaultCubeHash | Uses default boost::hash combine to hash Cubes |
| Ccore::sequence::SequenceAlignmentHasher | |
| Ccore::pose::UnrecognizedAtomRecord | Info about an atom in a unrecognized res (not in pose, but we want to remember it) |
| Ccore::fragment::picking_old::vall::scores::VallFragmentScore | Base Vall FragmentScore struct |
| Ccore::fragment::picking_old::vall::VallResidue | Class for managing a line of the Vall fragment library |
| Ccore::scoring::vdwaals::VDWAtom | |
| Ccore::scoring::vdwaals::VDWTrieEvaluator | |
| ►Cstd::vector< T > | STL class |
| Ccore::pose::Remarks | |
| ►Cutility::vector1< FrameOP > [external] | |
| Ccore::fragment::FrameList | |
| ►Cutility::vector1< MotifHit > [external] | |
| Ccore::scoring::motif::MotifHits | |
| ►Cutility::vector1< ResPairMotif > [external] | |
| Ccore::scoring::motif::ResPairMotifs | |
| ►Cutility::vector1< VallResidue > [external] | |
| Ccore::fragment::picking_old::vall::VallResidues | Wrapper for a collection of VallResidue |
| ►Cutility::vector1< VallSection > [external] | |
| Ccore::fragment::picking_old::vall::VallSections | Wrapper for a collection of VallSection |
| Ccore::conformation::symmetry::VirtualCoordinate | |
| Ccore::conformation::symmetry::VirtualCoordinates | |
| Ccore::scoring::methods::WaterBuilder | |
| Ccore::scoring::elec::weight_triple | |
| ►Cutility::factory::WidgetRegistrator< ConstraintFactory, T > [external] | |
| Ccore::scoring::constraints::ConstraintRegistrator< T > | This templated class will register an instance of an ConstraintCreator (class T) with the ConstraintFactory. It will ensure that no ConstraintCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| ►Cutility::factory::WidgetRegistrator< ResFilterFactory, T > [external] | |
| Ccore::pack::task::operation::ResFilterRegistrator< T > | This templated class will register an instance of an ResFilterCreator (class T) with the ResFilterFactory. It will ensure that no ResFilter creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| ►Cutility::factory::WidgetRegistrator< ResidueSelectorFactory, T > [external] | |
| Ccore::pack::task::residue_selector::ResidueSelectorRegistrator< T > | This templated class will register an instance of an ResidueSelectorCreator (class T) with the ResidueSelectorFactory. It will ensure that no ResidueSelector creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| ►Cutility::factory::WidgetRegistrator< ResLvlTaskOperationFactory, T > [external] | |
| Ccore::pack::task::operation::ResLvlTaskOperationRegistrator< T > | This templated class will register an instance of an ResLvlTaskOperationCreator (class T) with the ResLvlTaskOperationFactory. It will ensure that no ResLvlTaskOperation creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| ►Cutility::factory::WidgetRegistrator< ScoringManager, T > [external] | |
| Ccore::scoring::methods::EnergyMethodRegistrator< T > | This templated 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 |
| ►Cutility::factory::WidgetRegistrator< SequenceFactory, T > [external] | |
| Ccore::sequence::SequenceRegistrator< T > | This templated class will register an instance of an SequenceCreator (class T) with the SequenceFactory. It will ensure that no SequenceCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| ►Cutility::factory::WidgetRegistrator< SilentStructFactory, T > [external] | |
| Ccore::io::silent::SilentStructRegistrator< T > | This templated class will register an instance of an SilentStructCreator (class T) with the SilentStructFactory. It will ensure that no SilentStructCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| ►Cutility::factory::WidgetRegistrator< TaskOperationFactory, T > [external] | |
| Ccore::pack::task::operation::TaskOperationRegistrator< T > | This templated class will register an instance of an TaskOperationCreator (class T) with the TaskOperationFactory. It will ensure that no TaskOperation creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| Ccore::scoring::motif::Xfrag | |
| Ccore::scoring::motif::Xfres | |
| ►Ccore::scoring::func::XYZ_Func | Just a simple class that takes an AtomID and returns a Vector (position) |
| Ccore::scoring::func::ConformationXYZ | |
| Ccore::scoring::func::FourPointsFunc | A simple class that represents the coordinates of four points, pretending that they all belong to residue 1. The residue() method is not implemented and cause a utility_exit |
| Ccore::scoring::func::ResiduePairXYZ | |
| Ccore::scoring::func::ResidueXYZ | |
| ►Cnumeric::geometry::hashing::xyzStripeHash [external] | |
| Ccore::pose::xyzStripeHashPose | |
| ►Cnumeric::xyzVector< float > [external] | |
| Ccore::scoring::sc::Atom | |
| ►CE | |
| ►Ccore::pack::interaction_graph::FirstClassEdge< V, E, G > | |
| Ccore::pack::interaction_graph::HPatchEdge< V, E, G > | Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast |
| Ccore::pack::interaction_graph::SurfaceEdge< V, E, G > | Defines a Surface edge which will be used in determining surface energy |
| ►CV | |
| ►Ccore::pack::interaction_graph::FirstClassNode< V, E, G > | |
| Ccore::pack::interaction_graph::HPatchNode< V, E, G > | Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph |
| Ccore::pack::interaction_graph::SurfaceNode< V, E, G > | Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph |
1.8.7