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Rosetta 3.5
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Rosetta 3.5
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  boost | |
  tuples | |
  unordered_object_pool | |
| core | A class for defining atom parameters, known as atom_types |
| chemical | |
| carbohydrates | |
| CarbohydrateInfo | |
| orbitals | |
| AssignOrbitals | |
| ICoorOrbitalData | |
| OrbitalType | |
| OrbitalTypeMapper | |
| OrbitalTypeSet | |
| rna | |
| RNA_ResidueType | |
| sdf | |
| addedH | |
| elementToType | |
| CtabBase | |
| ctabV2000Parser | |
| ctabV3000Parser | |
| atomTyper | |
| MolFileParser | |
| BondData | |
| MolWriter | |
| MolData | |
| SDFParser | |
| V2Parser | |
| V3Parser | |
| Adduct | Description of optional single-atom residue adducts |
| Atom | Basic chemical atom |
| ICoorAtomID | Atom 's ID in internal coordinates in a ResidueType |
| AtomICoor | A basic class containing info of internal coordinates needed for building an atom within a ResidueType |
| AtomType | Basic atom type |
| AtomTypeDatabaseIO | |
| AtomTypeSet | Set of AtomTypes |
| AutomorphismIterator | Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations |
| ChemicalManager | Class managing different sets of atom_type_set and residue_type_set |
| CSDAtomType | Basic "conformational" atom type derived from analysis of Cambridge Structure Database |
| CSDAtomTypeSet | A set of CSDAtomTypes |
| Element | Class to describe Elements |
| ElementSet | A set of Elements |
| IdealBondLengthSet | A set of Elements |
| MMAtomType | Basic MM atom type |
| MMAtomTypeSet | A set of MMAtomTypes |
| Orbital | Basic chemical atom |
| PatchCase | A single case of a patch, eg proline Nterminus is a case of NtermProteinFull |
| Patch | A class patching basic ResidueType to create variant types, containing multiple PatchCase |
| PatchOperation | A single operation that needs to be applied in a residue patch |
| DeleteAtom | Delete an atom |
| SetBackboneHeavyatom | Set an atom as backbone heavy atom |
| SetPolymerConnectAtom | Set an atom as polymer connection |
| AddConnect | |
| AddProperty | Add a property to ResidueType |
| 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) |
| AddChi | Add a chi angle to ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's, which often result in one or more extra chi angles |
| AddProtonChi | |
| RedefineChi | Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTM's |
| AddChiRotamer | Add a rotamer sample to a chi angle of the ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's |
| AddAtom | Add an atom to ResidueType |
| AddBond | Add a bond to ResidueType |
| SetAtomicCharge | Set an atom's charge |
| SetAtomType | Set atom's chemical type |
| SetIO_String | Set atom's chemical type |
| SetMMAtomType | Set atom's MM chemical type |
| SetICoor | Set an atom's AtomICoord |
| PrependMainchainAtom | Add a mainchain atom before the first mainchain atom |
| AppendMainchainAtom | Add a mainchain atom after the last mainchain atom |
| SetNbrAtom | Set the residue neighbor atom |
| SetNbrRadius | Set the residue neighbor radius |
| SetOrientAtom | Set orient atom selection mode |
| NCAARotLibPath | Set the path to a rotamer library for an NCAA that is not in dunbrack |
| 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 |
| ResidueConnection | A simple class marking atoms at inter-residue connections |
| ResidueDatabaseIO | |
| ResidueLoader | |
| ResidueLoaderCreator | |
| ResidueLoaderOptions | |
| ResidueLoaderOptionsCreator | |
| ResidueSelectorSingle | A base class for defining a ResidueSelector by a single criterion |
| Selector_AA | Does the residue belong to ANY of these AAs? |
| 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 |
| Selector_NAME3 | Does the residue have to ANY of these three-letter codes? |
| Selector_PROPERTY | Does the residue have ANY of these properties? |
| Selector_VARIANT_TYPE | Does the residue have ANY of variant types? |
| Selector_MATCH_VARIANTS | Does the residue have ALL of the variant types and no more |
| Selector_NO_VARIANTS | Does the residue have ANY of variant types? |
| Selector_NAME1 | Does the residue belong to ANY of these AAs? |
| ResidueSelector | A class picking out a subset of ResidueType by multiple criteria |
| ResidueType | Silly demo class – what would the most familiar residue look like? |
| ResidueTypeSet | A collection of ResidueType defined |
| coarse | |
| CoarseEtable | |
| Rule | |
| BeadAdder | |
| GenericRule | |
| RuleSet | |
| Translator | |
| BeadAtom | |
| TranslatorSet | |
| conformation | |
| orbitals | |
| OrbitalXYZCoords | |
| RotamerSetCacheableDataType | |
| signals | |
| ConnectionEvent | Signal a change in the connection with a Conformation object, e.g. destruction or transfer |
| GeneralEvent | Signals a general change in a Conformation |
| IdentityEvent | Signals a change in residue identity in a Conformation |
| LengthEvent | Signals a change in length of residues in a Conformation |
| XYZEvent | Signals a change in XYZ coordinates in a Conformation |
| symmetry | |
| SymDof | |
| SymmData | |
| SymmDataFactory | |
| SymmDataLoader | |
| SymmDataLoaderCreator | |
| SymmDataOptions | |
| SymmDataOptionsCreator | |
| SymmetricConformation | A symmetric conformation: has an additional data member "SymmetryInfo" class |
| SymmetryInfo | |
| SymSlideInfo | |
| VirtualCoordinate | |
| VirtualCoordinates | |
| AbstractRotamerTrie | |
| Atom | A simple object with atom's position and its chemical type |
| AtomGraphVertexData | |
| AtomGraphEdgeData | |
| Conformation | A container of Residues and the kinematics to manage them |
| DefaultCubeHash | Uses default boost::hash combine to hash Cubes |
| AddEdgeVisitor | |
| PointGraphVertexData | |
| PointGraphEdgeData | |
| PseudoBond | |
| PseudoBondCollection | |
| Residue | Instance Residue class, used for placed residues and rotamers |
| ResidueFactory | Collection of functions making a single residue |
| ResidueKinWriter | |
| ConformationKinWriter | |
| ResidueMatcher | |
| WatsonCrickResidueMatcher | |
| ExactResidueMatcher | |
| RotamerSetBase | |
| fragment | |
| picking_old | |
| concepts | |
| Book | Forward declaration for Book |
| Book_VallResidues | |
| Bookmark | Forward declaration for core::fragment::picking_old::concepts::Bookmark |
| Extent | Forward declaration for Extent |
| ExtentEvaluator | Forward declaration for core::fragments::picking_old::concepts::ExtentEvaluator |
| ExtentGenerator | Forward declaration for core::fragment::picking_old::concepts::ExtentGenerator |
| Librarian | Forward declaration for core::fragment::picking_old::concepts::Librarian |
| Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary | |
| Library | Forward declaration for Library |
| Library_VallSections | |
| vall | |
| eval | |
| ABEGOEval | Scores a fragment based on sum of secondary structure identity and sequence identity |
| EnergyEval | Scores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction |
| IdentityEval | Scores a fragment based on sum of secondary structure identity and sequence identity |
| VallFragmentEval | Base class for Vall ExtentEvaluator |
| gen | |
| LengthGen | Default constant length fragment Vall ExtentGenerator |
| SecStructGen | Generator that requires fragments to have a specific secondary structure string |
| VallFragmentGen | Base class Vall ExtentGenerator |
| scores | |
| VallFragmentScore | Base Vall FragmentScore struct |
| VallLibrarian | Librarian that picks fragments from the Vall |
| VallLibrary | Vall fragment library |
| VallResidue | Class for managing a line of the Vall fragment library |
| VallResidues | Wrapper for a collection of VallResidue |
| VallSection | Class implementing the Book concept for a continuous section of lines in the Vall library |
| VallSections | Wrapper for a collection of VallSection |
| FragmentLibraryManager | Singleton class for accessing fragment libraries |
| BaseCacheUnit | |
| BBTorsionAndAnglesSRFD | |
| BBTorsionSRFD | |
| ConstantLengthFragSet | A set of fragments that contains fragments of a constant length read in from a fragment file |
| ConstantLengthFragSetIterator_ | |
| FragCache | |
| MapCacheUnit | |
| VectorCacheUnit | |
| CacheWrapper | |
| FragStore | |
| FragData | |
| AnnotatedFragData | FragData that contains additional information |
| FragID | |
| FragID_Iterator | |
| FragFactory | |
| FragmentIO | |
| FragmentRmsd | |
| FragSet | The FragSet: (Interface Definition – Virtual BaseClass ) |
| FragSetCollection | |
| Frame | Frame couples a list of FragData-instances to a certain alignment frame, i.e., position in sequence space A frame may be continous, i.e., its fragment data will be applied to all residues between start() and end() or ( in a specialized version inheriting this interface) may contain a loose list of sequence positions |
| FrameIterator | |
| FrameIteratorWorker_ | |
| FrameList | |
| FrameListIterator_ | |
| 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) |
| 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! |
| 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 |
| UpJumpSRFD | |
| DownJumpSRFD | |
| OrderedFragSet | |
| OrderedFragSetIterator_ | |
| 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, |
| SecstructSRFD | |
| SingleResidueFragData | Base class for SRFD classes Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position |
| TorsionInfoSet | |
| graph | |
| Array0 | 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 |
| NegSpaceElement | NegSpaceElement represents a single element in the singly-linked list of negative space in an array pool |
| ArrayPoolElement | |
| ArrayPool | |
| DS_Node | |
| DisjointSets | |
| EdgeListElement | An extensible graph class |
| 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 * > |
| 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 * > |
| 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 |
| Node | |
| Edge | |
| Graph | A Graph with constant time edge insertion and deletion. Extensible |
| UEVertex | |
| UEEdge | |
| UpperEdgeGraph | |
| grid | |
| CartGrid | |
| id | |
| AtomID | Atom identifier class. Defined by the atom number and the residue number |
| BondID | Two more classes, temporary for testing purposes |
| StubID | |
| AtomID_Map | Map from Atom identifiers to contained values class |
| CacheableAtomID_MapVector | AtomID_Map< xyzVector< Real > > |
| DOF_ID | Kinematics DOF identifier class |
| DOF_ID_Map | Map from Atom DOF identifiers to contained values class |
| DOF_ID_Range | Kinematics DOF identifier (with range) class |
| EXCN_AtomNotFound | |
| JumpID | |
| NamedAtomID | Atom identifier class |
| NamedStubID | |
| SequenceMapping | |
| TorsionID | |
| TorsionID_Range | Kinematics DOF identifier (with range) class |
| import_pose | |
| atom_tree_diffs | |
| ScoreLessThanComparator | Provides a StrictWeakOrdering comparator for sorting elements of a ScoresMap by one particular score type |
| AtomTreeDiff | An object wrapper for reading atom_tree_diff files, complete with embedded reference structures |
| pose_stream | |
| ExtendedPoseInputStream | |
| LazySilentFilePoseInputStream | |
| MetaPoseInputStream | |
| PDBPoseInputStream | |
| PoseInputStream | |
| PoseOutputStream | |
| SilentFilePoseInputStream | |
| 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! |
| ImportPoseOptionsCreator | |
| PDBSilentStruct | |
| PDBSilentStructCreator | Creator for the PDBSilentStruct class |
| PoseFromPDBLoader | |
| PoseFromPDBLoaderCreator | |
| io | |
| pdb | |
| Field | Data type Class to represent one field in PDB file |
| AtomInformation | A class that contains information for individual atoms |
| ResidueInformation | Intermediate format for easy construction of core::conformation::Residue objects |
| LinkInformation | A structure for storing information from PDB LINK records |
| FileData | FileData class. Hold data created from PDB file |
| FileDataOptions | |
| HeaderInformation | Information stored in the header records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z |
| PDB_DReader | PDB Reader it self, D - for dynamic approch of type handling |
| PDB_DReaderOptions | |
| 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.. |
| raw_data | |
| DecoyFileData | |
| DecoyStruct | |
| DisulfideFile | Parses and stores a disulfide file |
| ResNum | Residue of either pdb or rosetta numbering |
| 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 |
| const_iterator | Const_iterator class for RawFileData container |
| iterator | Iterator class for RawFileData container |
| RawStruct | |
| ScoreFileData | |
| ScoreStruct | |
| 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 |
| serialization | |
| BUFFER | |
 silent | |
 ProteinSilentStruct_SinglePrecCreator | Creator for the ProteinSilentStruct_SinglePrec class |
| ProteinSilentStructCreator | Creator for the ProteinSilentStruct class |
| RNA_SilentStructCreator | Creator for the RNA_SilentStruct class |
| BinaryProteinSilentStructCreator | Creator for the BinaryProteinSilentStruct class |
| ScoreFileSilentStructCreator | Creator for the ScoreFileSilentStruct class |
| BinaryRNASilentStructCreator | Creator for the BinaryRNASilentStruct class |
| BinaryProteinSilentStruct | Why this inheritance pathway? this makes no sense! |
| BinaryRNASilentStruct | |
| EnergyNames | |
| ProteinSilentStruct_Template | |
| RNA_SilentStruct | |
| ScoreFileSilentStruct | |
| SharedSilentData | |
| SimpleSequenceData | |
| SilentEnergy | Helper class for silent-file classes to keep track of energy information |
| 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 |
| const_iterator | Const_iterator class for SilentFileData container |
| iterator | Iterator class for SilentFileData container |
| SilentFileLoader | |
| SilentFileLoaderCreator | Creator for the SilentFileLoader class |
| SilentFileOptions | |
| SilentFileOptionsCreator | Creator for the SilentFileOptions class |
| SilentStruct | |
| SilentStructCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| SilentStructFactory | |
| SilentStructRegistrator | 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 |
| kinematics | See AtomTree overview and FoldTree overview for details |
| tree | |
| Atom | Kinematics Atom interface class |
| Atom_ | Kinematics Atom abstract base class |
| BondedAtom | Atom which are bonded to its parentt, derived from Atom_ |
| JumpAtom | Atom who are connected to its parent via rigid-body transformation "Jump" |
| AtomTree | Wrapper for a tree of kinematic Atoms |
| AtomWithDOFChange | Simple class for use in output-sensitive refold subroutine |
| Edge | Single edge of the fold_tree |
| EXCN_InvalidFoldTree | |
| FoldTree | The FoldTree is a residue-based treelike representation of a molecule |
| Jump | Object which makes rigid-body transformation with translational and rotational perturbation |
| MinimizerMapBase | |
| MoveMap | A class specifying DOFs to be flexible or fixed |
| 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 |
| RT | Rotation + translation class |
| ShortestPathInFoldTree | |
| Stub | Stub class – an object of orthogonal coordinate frame |
| Node | |
| TreeVizBuilder | |
| optimization | |
| symmetry | |
| MinDebug | |
| SymAtomTreeMinimizer | High-level atom tree minimizer class |
| SymAtomTreeMultifunc | Atom tree multifunction class |
| SymMinimizerMap | Atom tree multifunction class |
| AtomNode | |
| AtomTreeMinimizer | High-level atom tree minimizer class |
| AtomTreeMultifunc | Atom tree multifunction class |
| CartesianMinimizer | High-level atom tree minimizer class |
| CartesianMinimizerMap | |
| CartesianMultifunc | Atom tree multifunction class |
| DOF_Node | |
| EItem | Inner class for Genetic Algorithm, hold one population with some additional info |
| GA_Minimizer | |
| func_1d | |
| LineMinimizationAlgorithm | |
| BrentLineMinimization | |
| ArmijoLineMinimization | |
| StrongWolfeLineMinimization | |
| ConvergenceTest | |
| DFPMinConvergedFractional | |
| DFPMinConvergedAbsolute | |
| DescentDirectionAlgorithm | |
| JJH_Minimizer | |
| lbfgs_iteration_data | |
| Minimizer | Simple low-level minimizer class |
| MinimizerMap | |
| MinimizerOptions | |
| Multifunc | Multifunction interface class |
| DerivCheckDataPoint | |
| SimpleDerivCheckResult | |
| DOF_DataPoint | |
| NumDerivCheckData | |
| NumericalDerivCheckResult | |
| Particle | Simple data container for PSO algorithm |
| ParticleSwarmMinimizer | Particle Swarm Optimization engine |
| SingleResidueMultifunc | A streamlined AtomTreeMultifunc designed specifically for RTMIN |
| pack | |
| annealer | |
| AnnealerFactory | |
| DebuggingAnnealer | |
| FASTERAnnealer | |
| FixbbCoupledRotamerSimAnnealer | |
| FixbbLinkingRotamerSimAnnealer | |
| FixbbSimAnnealer | |
| MultiCoolAnnealer | |
| RotamerAssigningAnnealer | |
| SimAnnealerBase | |
| dunbrack | |
| ChiSet | |
| CoarseRotamer | |
| CoarseRotamerSet | |
| CoarseSingleResidueLibrary | |
| DunbrackConstraint | |
| DunbrackConstraintCreator | Mover creator for the DunbrackConstraint constraint |
| DunbrackEnergy | |
| DunbrackEnergyCreator | |
| DunbrackRotamerMeanSD | Forward declaration; default precision is DunbrackReal |
| PackedDunbrackRotamer | Forward declaration; default precision is DunbrackReal; |
| DunbrackRotamer | Forward declaration; default precision is DunbrackReal |
| DunbrackRotamerSampleData | |
| 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 |
| RotamerConstraint | This class favors a particular rotamer at a particular position by reducing its Dunbrack energy |
| RotamericSingleResidueDunbrackLibrary | |
| RotamericData | |
| SingleResidueRotamerLibrary | |
| RotamerLibrary | |
| RotamerLibraryScratchSpace | |
| SemiRotamericSingleResidueDunbrackLibrary | 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 |
| BBDepNRChiSample | P for precision |
| BBIndNRChiSample | |
| BBDepSemiRotamericData | 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 |
| BBDepScoreInterpData | |
| BBIndSemiRotamericData | 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 |
| ProbSortClass | |
| SingleLigandRotamerLibrary | A fixed library of conformations for some residue type (doesn't have to be a ligand) |
| SingleResidueDunbrackLibraryConcrete | |
| SingleResidueDunbrackLibrary | |
| interaction_graph | |
| FirstClassNode | |
| FirstClassEdge | |
| BackgroundNode | A node which is not changing type or rotamer throughout a simulation |
| BackgroundToFirstClassEdge | An edge between a background node and a first class node |
| AdditionalBackgroundNodesInteractionGraph | Function declarations for the AdditionalBackgroundNodesInteractionGraph |
| AminoAcidNeighborSparseMatrix | |
| DensePDNode | |
| DensePDEdge | |
| DensePDInteractionGraph | |
| DoubleDensePDNode | |
| DoubleDensePDEdge | |
| DoubleDensePDInteractionGraph | |
| DoubleLazyNode | |
| DoubleLazyEdge | |
| 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 |
| FASTERNode | |
| FASTEREdge | |
| FASTERInteractionGraph | |
| FixedBBNode | |
| FixedBBEdge | |
| FixedBBInteractionGraph | |
| 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 |
| HPatchEnergyCreator | |
| HPatchInteractionGraph | Defines the interaction graph that will keep track of changes to the hpatch score |
| exposed_hydrophobic_data | |
| HPatchNode | Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph |
| HPatchBackgroundNode | 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 |
| HPatchEdge | 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 |
| HPatchBackgroundEdge | Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) |
| NodeBase | |
| EdgeBase | |
| InteractionGraphBase | |
| InteractionGraphFactory | |
| LazyNode | |
| LazyEdge | |
| LazyInteractionGraph | |
| history_queue_struct | For storing three peices of associated data describing the recent history structure on a LinearMemNode |
| LinearMemNode | |
| LinearMemEdge | |
| LinearMemoryInteractionGraph | |
| OnTheFlyNode | |
| OnTheFlyEdge | |
| OnTheFlyInteractionGraph | |
| PDNode | |
| PDEdge | |
| PDInteractionGraph | |
| PrecomputedPairEnergiesNode | |
| PrecomputedPairEnergiesEdge | |
| PrecomputedPairEnergiesInteractionGraph | |
| DotSphere | Represents the sphere of dots on the vdW surface of an atom, for use in the LeGrand and Merz method of calculating SASA |
| RotamerDots | Handles sphere-sphere overlap calculations for the HPatchInteractionGraph |
| RotamerDotsRadiusData | A singleton class which reads in database SASA radii files and provides accessors for those values to the RotamerDots class |
| RotamerDotsCache | A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes |
| InvRotamerDots | Used to determine whether the overlap between two atoms is buried or exposed |
| SimpleNode | |
| SimpleEdge | |
| 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 |
| SparseMatrixIndex | |
| 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 |
| SurfaceEnergyCreator | |
| SurfaceInteractionGraph | Defines the interaction graph that will keep track of changes to the surface score |
| SurfaceNode | Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph |
| SurfaceBackgroundNode | 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 |
| SurfaceEdge | Defines a Surface edge which will be used in determining surface energy |
| SurfaceBackgroundEdge | Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) |
| SurfacePotential | |
| SymmLinearMemNode | |
| SymmLinearMemEdge | |
| SymmLinearMemoryInteractionGraph | |
| SymmMinimalistNode | |
| SymmMinimalistEdge | |
| SymmMinimalistInteractionGraph | |
| SymmOnTheFlyNode | |
| SymmOnTheFlyEdge | |
| SymmOnTheFlyInteractionGraph | |
| 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_ |
| SymmetricRotamerSetFactory | |
| SymmetricRotamerSets | |
| BumpSelector | |
| ContinuousRotamerSet | |
| ContinuousRotamerSets | |
| FixbbRotamerSets | |
| RotamerCouplings | |
| RotamerLinks | |
| RotamerSet | |
| 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 |
| RotamerSetFactory | |
| RotamerOperation | RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation |
| RotamerSetOperation | |
| RotamerSets | |
| RotamerSetsBase | |
| 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) |
| RotamerSubsets | |
| UnboundRotamersOperation | Adds in rotamers from the "unbound" or native structure(s), pulled from one or more PDBs supplied on the command line |
| WaterAnchorInfo | |
| WaterPackingInfo | |
| scmin | |
| ResidueAtomTreeCollectionMomento | Class to save the state for a ResidueAtomTreeCollection |
| 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 |
| AtomTreeCollection | A collection of ResidueAtomTreeCollection objects for an entire design task |
| AtomTreeSCMinMinimizerMap | |
| CartSCMinMinimizerMap | |
| CartSCMinMultifunc | |
| SCMinMinimizerMap | |
| SCMinMultifunc | |
| SidechainStateAssignment | |
| task | |
| operation | |
| util | |
| NoRepackDisulfides | Prevent disulfides from being repacked; assume disulfides info in Pose is up-to-date |
| NoRepackDisulfidesCreator | |
| OperateOnCertainResidues | |
| OperateOnCertainResiduesCreator | |
| 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() |
| OptCysHGCreator | |
| OptH | Run optH; disallowed positions may be set to prevent optimization for those residues |
| OptHCreator | |
| ReplicateTask | |
| ReplicateTaskCreator | |
| ResFilter | |
| 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 |
| AnyResFilterCreator | |
| AllResFilterCreator | |
| NoResFilterCreator | |
| ResidueTypeFilterCreator | |
| ResidueHasPropertyCreator | |
| ResidueLacksPropertyCreator | |
| ResidueName3IsCreator | |
| ResidueName3IsntCreator | |
| ResidueIndexIsCreator | |
| ResidueIndexIsntCreator | |
| ResiduePDBIndexIsCreator | |
| ResiduePDBIndexIsntCreator | |
| ChainIsCreator | |
| ChainIsntCreator | |
| ResFilterFactory | |
| ResFilterRegistrator | 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 |
| ResFilterComposition | |
| AnyResFilter | |
| AllResFilter | |
| NoResFilter | |
| ResidueTypeFilter | |
| ResidueHasProperty | |
| ResidueLacksProperty | |
| ResidueName3Is | |
| ResidueName3Isnt | |
| ResidueIndexIs | |
| ResidueIndexIsnt | |
| ResiduePDBIndexIs | |
| ChainPos | |
| ResiduePDBIndexIsnt | |
| ChainIs | |
| ChainIsnt | |
| ResLvlTaskOperation | |
| 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 |
| RestrictToRepackingRLTCreator | |
| RestrictAbsentCanonicalAASRLTCreator | |
| DisallowIfNonnativeRLTCreator | |
| PreventRepackingRLTCreator | |
| AddBehaviorRLTCreator | |
| ResLvlTaskOperationFactory | |
| ResLvlTaskOperationRegistrator | 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 |
| RestrictToRepackingRLT | |
| RestrictAbsentCanonicalAASRLT | |
| DisallowIfNonnativeRLT | |
| PreventRepackingRLT | |
| AddBehaviorRLT | |
| DockingNoRepack1 | |
| DockingNoRepack2 | |
| RestrictToInterface | |
| TaskOperation | |
| 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 |
| RestrictYSDesignCreator | |
| PreventRepackingCreator | |
| PreserveCBetaCreator | |
| AppendRotamerSetCreator | |
| AppendResidueRotamerSetCreator | |
| AppendRotamerCreator | |
| SetRotamerCouplingsCreator | |
| SetRotamerLinksCreator | |
| ReadResfileCreator | |
| ReadResfileAndObeyLengthEventsCreator | |
| IncludeCurrentCreator | |
| InitializeExtraRotsFromCommandlineCreator | |
| InitializeFromCommandlineCreator | |
| ExtraRotamersGenericCreator | |
| RotamerExplosionCreator | |
| RestrictAbsentCanonicalAASCreator | |
| RestrictResidueToRepackingCreator | |
| RestrictToRepackingCreator | |
| DisallowIfNonnativeCreator | |
| ExtraRotamersCreator | |
| ExtraChiCutoffCreator | |
| TaskOperationFactory | |
| TaskOperationRegistrator | 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 |
| RestrictToRepacking | |
| RestrictResidueToRepacking | RestrictResidueToRepacking |
| RestrictAbsentCanonicalAAS | |
| 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 |
| RotamerExplosion | Rotamer explosion for a residue |
| InitializeFromCommandline | |
| InitializeExtraRotsFromCommandline | |
| IncludeCurrent | |
| ExtraRotamersGeneric | |
| ReadResfile | |
| 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 |
| SetRotamerCouplings | |
| SetRotamerLinks | |
| AppendRotamer | When a PackerTask is created by the Factory, the RotamerOperation will be given to it |
| AppendRotamerSet | When a PackerTask is created by the Factory, the RotamerSetOperation will be given to it |
| AppendResidueRotamerSet | Apply rotamerSetOperation to only the rotamerSet for the given residue |
| PreserveCBeta | |
| 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 |
| RestrictYSDesign | RestrictYSDesign restricts positions to a binary Tyr/Ser alphabet |
| ExtraRotamers | ExtraRotamer for a residue. You know, -ex1, -ex2, all that |
| ExtraChiCutoff | ExtraChiCutoff (correponding to flag "-extrachi_cutoff <float>" ) |
| IGEdgeReweighter | Helper class for IGEdgeReweightContainer |
| IGEdgeReweightContainer | Class that interfaces to containers holding IGedge weights between individual residues of the task |
| ResidueLevelTask | |
| PackerTask | Task class that gives instructions to the packer |
| ResidueLevelTask_ | Residue-level task class; contained within PackerTask |
| PackerTask_ | PackerTask controls what rotameric (including sequence) changes the packer is allowed to make |
| ResfileReaderException | |
| ResfileContents | |
| ResfileCommand | Abstract/interface class for Resfile reader command objects |
| NATRO | NATRO disables packing and designing at a position, the residue will be totally unchanged |
| NATAA | NATAA allows repacking but no sequence changes (all rotamers are of the original residue) |
| ALLAA | ALLAA is deprecated; allows repacking and designing to any canonical residue (default state of PackerTask) |
| ALLAAxc | ALLAAxc allows repacking and designing to any canonical noncysteine residue |
| ALLAAwc | Allows repacking and designing to any canonical residue (default state of PackerTask) |
| PIKAA | PIKAA allows residues specifed in a following string and packing |
| PIKNA | PIKNA allows nucleic acid residues specifed in a following string |
| PIKRNA | PIKRNA allows nucleic acid residues specifed in a following string |
| NOTAA | NOTAA disallows residues specified in a following string, and allows packing |
| EMPTY | EMPTY disallows all canonical residues but leaves packing and designing unchanged (for noncanonicals) |
| POLAR | POLAR allows polar residues and packing |
| APOLAR | APOLAR allows nonpolar residues and packing |
| APOLA | APOLA is deprecated, it calls APOLAR to allow nonpolar residues and packing |
| EX | EX handles the various extrachi options |
| NC | NC handles explicit allowance of noncanonical residue types |
| EX_CUTOFF | EX_CUTOFF allows setting of the extrachi_cutoff (for determining burial for extra rotamers) |
| USE_INPUT_SC | USE_INPUT_SC turns on inclusion of the current rotamer for the packer |
| AUTO | AUTO suggests that a packer can/should reconsider the design setting at a/each residue |
| 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 |
| TARGET | TARGET flags the position as "targeted", and can optionally specify a "targeted" type |
| 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 |
| 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) |
| TaskFactory | Factory class for the creation and initialization of PackerTask objects |
| RTMin | |
| pose | |
| carbohydrates | |
| datacache | |
| LengthEventCollector | Cacheable observer that keeps track of what length events occured |
| 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 |
| CacheableDataType | |
| CacheableObserver | Base class for Pose/Conformation observers that are stored in a Pose's DataCache |
| CacheableObserverType | |
| CacheablePoseRawPtr | Pose * |
| ObserverCache | A DataCache storing Pose/Conformation observers derived from core::pose::datacache::CacheableObserver |
| PositionConservedResiduesStore | |
| metrics | |
| simple_calculators | |
| InterfaceDefinitionCalculator | |
| InterfaceDeltaEnergeticsCalculator | |
| InterfaceNeighborDefinitionCalculator | |
| InterfaceSasaDefinitionCalculator | |
| SasaCalculator | |
| CalculatorFactory | |
| PoseMetricCalculator | |
| StructureDependentCalculator | |
| EnergyDependentCalculator | |
| PoseMetricContainer | Container for managing PoseMetricCalculators |
| signals | |
| ConformationEvent | Signals a conformation change in a Pose |
| DestructionEvent | Special signal that the Pose is getting destroyed |
| EnergyEvent | Signals an energy change in a Pose |
| GeneralEvent | Signals a general change in a Pose |
| symmetry | |
| MiniPose | |
| UnrecognizedAtomRecord | Info about an atom in a unrecognized res (not in pose, but we want to remember it) |
| PDBInfo | Maintains pdb residue & atom information inside a Pose |
| AtomRecord | Internal struct for storing PDB atom related information |
| ResidueRecord | Internal struct for storing PDB residue related information |
| 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 |
| ResidueKey | Sortable residue key internal to PDBPoseMap |
| Pose | A molecular system including residues, kinematics, and energies |
| RemarkInfo | |
| Remarks | |
| scoring | |
| carbon_hbonds | |
| CarbonHBondEnergy | |
| CarbonHBondEnergyCreator | |
| CarbonHBondPotential | |
| constraints | |
| AmberPeriodicFunc | Function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) |
| AmbiguousConstraint | |
| AmbiguousNMRConstraint | |
| AmbiguousNMRDistanceConstraint | |
| AngleConstraint | An Angular Constraint |
| AtomPairConstraint | |
| BackboneStubConstraint | This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location |
| AtomPairConstraintCreator | Mover creator for the AtomPairConstraint constraint |
| AngleConstraintCreator | Mover creator for the AngleConstraint constraint |
| DihedralConstraintCreator | Mover creator for the DihedralConstraint constraint |
| DihedralPairConstraintCreator | Constraint creator for DihedralPairConstraint |
| BigBinConstraintCreator | Mover creator for the BigBinConstraint constraint |
| MultiConstraintCreator | Mover creator for the MultiConstraint constraint |
| AmbiguousConstraintCreator | Mover creator for the AmbiguousConstraint constraint |
| KofNConstraintCreator | Mover creator for the KofNConstraint constraint |
| CoordinateConstraintCreator | Mover creator for the CoordinateConstraint constraint |
| LocalCoordinateConstraintCreator | Mover creator for the LocalCoordinateConstraint constraint |
| AmbiguousNMRDistanceConstraintCreator | Mover creator for the AmbiguousNMRDistanceConstraint constraint |
| AmbiguousNMRConstraintCreator | Mover creator for the AmbiguousNMRConstraint constraint |
| SiteConstraintCreator | Mover creator for the SiteConstraint constraint |
| SiteConstraintResiduesCreator | Mover creator for the SiteConstraintResidues constraint |
| FabConstraintCreator | Mover creator for the FabConstraint constraint |
| BigBinConstraint | Constraint on dihedral angle formed by 4 points |
| BoundFunc | |
| PeriodicBoundFunc | Variant of the bound func that is periodic |
| OffsetPeriodicBoundFunc | Variant of the bound func that is periodic |
| CharmmPeriodicFunc | Function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) |
| CircularGeneral1D_Func | Function that allows return of arbitrary FArrays – this time circularized |
| CircularHarmonicFunc | Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints |
| CircularPowerFunc | Generalization of CircularCircularPowerFunc – other exponents allowed |
| CircularSigmoidalFunc | Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints |
| ConstantConstraint | A Constant Constraint |
| ConstantFunc | Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation |
| Constraint | Actually a restraint, like a virtual rubber band between a pair of atoms |
| ConstraintCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| CstResNeighbIterator | |
| CstResNeighbConstIterator | |
| CstEnergyContainer | |
| ConstraintFactory | |
| ConstraintRegistrator | 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 |
| ConstraintNode | |
| ConstraintEdge | |
| ConstraintGraph | |
| ConstraintIO | |
| Constraints | |
| ConstraintsEnergy | |
| ConstraintsEnergyCreator | |
| ResidueConstraints | |
| ConstraintSet | |
| CoordinateConstraint | |
| CountViolFunc | |
| CstMinimizationData | |
| DihedralConstraint | Constraint on dihedral angle formed by 4 points |
| DihedralPairConstraint | Constraint on dihedral angle formed by 4 points |
| DistancePairConstraint | Constraint on CA distance |
| DOF_Constraint | This isn't quite a standard constraint since it acts on DOF's directly rather than on XYZ coordinates |
| EtableFunc | Class for representing arbitrarily defined functions |
| FabConstraint | |
| FadeFunc | |
| FlatHarmonicFunc | |
| 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 |
| 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 |
| FuncFactory | |
| GaussianFunc | Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation |
| HarmonicFunc | |
| IdentityFunc | |
| 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 |
| KofNConstraint | |
| LinearPenaltyFunction | |
| LocalCoordinateConstraint | |
| MinMultiHarmonicFunc | |
| 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 |
| MultiConstraint | |
| Obsolet_NamedAtomPairConstraint | |
| NamedAtomPairConstraint | |
| NonResidueTypeConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| PeriodicFunc | Function of type y = ( k * cos(n * (x - x0) ) ) + C |
| ResidueTypeConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| ResidueTypeLinkingConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| ScalarWeightedFunc | |
| SequenceProfileConstraint | |
| SequenceProfileConstraintCreator | Constraint creator for the SequenceProfileConstraint constraint |
| SigmoidFunc | |
| SiteConstraint | |
| SiteConstraintResidues | |
| SkipViolFunc | |
| SoedingFunc | Derived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation |
| SOGFunc | Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation |
| SOGFunc_Impl | Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation |
| SplineFunc | |
| SquareWell2Func | |
| SquareWellFunc | |
| SumFunc | |
| TopOutFunc | |
| USOGFunc | Unnormalized, unbounded sum of Gaussians constraint |
| XYZ_Func | Just a simple class that takes an AtomID and returns a Vector (position) |
| ResidueXYZ | |
| ResiduePairXYZ | |
| ConformationXYZ | |
| ChainbreakDistFunc | |
| custom_pair_distance | |
| RespairInteractions | |
| atoms_and_func_struct | |
| resatom_and_func_struct | |
| AtomPairFuncList | |
| FullatomCustomPairDistanceEnergy | |
| DistanceFunc | |
| FullatomCustomPairDistanceEnergyCreator | |
| disulfides | |
| CentroidDisulfideEnergy | |
| CentroidDisulfideNeighborIterator | An iterator over the disulfide bonds a residue forms |
| CentroidDisulfideNeighborConstIterator | Just a const version of CentroidDisulfideNeighborIterator |
| CentroidDisulfideEnergyComponents | Storage for Disulfide Energy Terms |
| CentroidDisulfideEnergyContainer | |
| CentroidDisulfideEnergyCreator | |
| CentroidDisulfidePotential | |
| Cb_Distance_Func | Score based on the distance between Cb |
| Cen_Distance_Func | |
| CaCbCb_Angle_Func | |
| NCaCaC_Dihedral_Func | |
| CaCbCbCa_Dihedral_Func | |
| 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 |
| DisulfideMatchingDatabase | |
| DisulfideMatchingEnergy | |
| DisulfideMatchingNeighborIterator | An iterator over the disulfide bonds a residue forms |
| DisulfideMatchingNeighborConstIterator | Just a const version of DisulfideMatchingNeighborIterator |
| DisulfideMatchingEnergyComponents | Storage for Disulfide Energy Terms |
| DisulfideMatchingEnergyContainer | |
| DisulfideMatchingEnergyCreator | |
| DisulfideMatchingPotential | |
| RT_helper | |
| DisulfMinData | |
| FullatomDisulfideEnergy | |
| DisulfResNeighbIterator | |
| DisulfResNeighbConstIterator | |
| FullatomDisulfideEnergyComponents | |
| FullatomDisulfideEnergyContainer | |
| FullatomDisulfideEnergyCreator | |
| FullatomDisulfidePotential | |
| CBSG_Dihedral_Func | |
| SGSG_Dihedral_Func | |
| CB_Angle_Func | |
| SG_Dist_Func | |
| dna | |
| BasePartner | Silly vector1 wrapper class so we can derive from PoseCachedData |
| DirectReadoutPotential | 1st pass implementation of Kono + Sarai's protein-DNA interaction potential |
| DNA_BasePotential | |
| TorsionFourierComponent | |
| DNABFormPotential | |
| DNAChiEnergy | |
| DNAChiEnergyCreator | |
| DNATorsionEnergy | |
| DNATorsionEnergyCreator | |
| DNATorsionPotential | |
| dssp | |
| Dssp | |
| Pairing | |
| StrandPairing | |
| StrandPairingSet | |
| electron_density | |
| SplineInterp | |
| ElecDensAllAtomCenEnergy | |
| ElecDensAllAtomCenEnergyCreator | |
| ElecDensCenEnergy | |
| ElecDensCenEnergyCreator | |
| ElecDensEnergy | |
| ElecDensEnergyCreator | |
| ElectronDensity | |
| ElectronDensityLoader | |
| ElectronDensityLoaderCreator | Creator for the ElectronDensityLoader class |
| ElectronDensityOptions | |
| ElectronDensityOptionsCreator | Creator for the ElectronDensityOptions class |
| FastDensEnergy | |
| FastDensEnergyCreator | |
| PattersonCorrEnergy | |
| PattersonCorrEnergyCreator | |
| KromerMann | |
| OneGaussianScattering | |
| electron_density_atomwise | |
| ElecDensAtomwiseEnergy | |
| ElecDensAtomwiseEnergyCreator | |
| ElectronDensityAtomwise | |
| EnergiesCacheableDataType | |
| etable | |
| count_pair | |
| CountPair1B | |
| CountPairAll | |
| CountPairCrossover3 | |
| CountPairCrossover4 | |
| CountPairFactory | |
| Invoker | |
| CountPairFunction | |
| CountPairGeneric | |
| CountPairIntraRes | |
| CountPairIntraResC3 | |
| CountPairIntraResC4 | |
| CountPairNone | |
| etrie | |
| CountPairData_1_1 | |
| CountPairData_1_2 | |
| CountPairData_1_3 | |
| GenericResidueConnectionData | |
| CountPairDataGeneric | |
| EtableAtom | |
| TrieCountPair1BC3 | |
| TrieCountPair1BC4 | |
| TrieCountPairAll | |
| TrieCountPairGeneric | |
| TrieCountPairNone | |
| AtomPairEnergy | |
| BaseEtableEnergy | |
| ResResEnergyInvoker | |
| WholeWholeEnergyInvoker | |
| SC_BB_EnergyInvoker | |
| SC_Whole_EnergyInvoker | |
| BB_BB_EnergyInvoker | |
| SC_SC_EnergyInvoker | |
| CoarseEtableEnergy | |
| CoarseEtableEnergyCreator | |
| SplineParameters | |
| ExtraQuadraticRepulsion | |
| EtableParamsOnePair | |
| Etable | Jk Class definition for Etable |
| EtableEvaluator | |
| AnalyticEtableEvaluator | |
| TableLookupEvaluator | |
| TableLookupEtableEnergy | |
| AnalyticEtableEnergy | |
| EtableEnergyCreator | |
| EtableOptions | |
| MembEtable | Jk Class definition for Etable |
| geometric_solvation | |
| ContextIndependentGeometricSolEnergy | |
| ContextIndependentGeometricSolEnergyCreator | |
| DatabaseOccSolEne | |
| GridInfo | |
| WaterWeightGridSet | |
| ExactOccludedHbondSolEnergy | |
| ExactOccludedHbondSolEnergyCreator | |
| GeometricSolEnergy | |
| GeometricSolEnergyCreator | |
| OccludedHbondSolEnergy | |
| OccludedHbondSolEnergy_onebody | |
| OccludedHbondSolEnergy_onebodyCreator | |
| OccludedHbondSolEnergyCreator | |
| hackaro | |
| HackAroEnergy | |
| HackAroEnergyCreator | |
| hackelec | |
| ElecAtom | |
| weight_triple | |
| HackElecEnergy | |
| HackElecEnergyAroAll | |
| HackElecEnergyAroAllCreator | |
| HackElecEnergyAroAro | |
| HackElecEnergyAroAroCreator | |
| HackElecEnergyCreator | |
| RNAHackElecEnergy | |
| RNAHackElecEnergyCreator | |
| hbonds | |
| hbtrie | |
| HBAtom | |
| HBCountPairFunction | |
| HBCPData | |
| FadeInterval | Classic FadeInterval |
| HBEvalTuple | |
| HBondDatabase | |
| HBondResidueMinData | A class to hold data for the HBondEnergy class used in score and derivative evaluation |
| HBondResPairMinData | |
| HBondEnergy | |
| HBondEnergyCreator | |
| HBondOptions | |
| HBond | |
| HBondSet | |
| HBondTypeManager | |
| Polynomial_1d | |
| HBondDerivs | |
| interface | |
| DDPlookup | |
| DDPscore | |
| DDPscoreCreator | |
| methods | |
| dfire | |
| DFIRE_Energy | |
| DFIRE_EnergyCreator | |
| DFIRE_Potential | |
| BurialEnergy | |
| BurialEnergyCreator | |
| CartBondedParameters | |
| BBIndepCartBondedParameters | |
| BBDepCartBondedParameters | |
| ResidueCartBondedParameters | |
| IdealParametersDatabase | |
| CartesianBondedEnergy | |
| CartesianBondedEnergyCreator | |
| CenHBEnergy | |
| CenHBEnergyCreator | |
| CenPairEnergy | |
| CenPairEnergyCreator | |
| ChainbreakEnergy | ChainbreakEnergy 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 |
| ChainbreakEnergyCreator | |
| ChemicalShiftAnisotropyEnergy | |
| ChemicalShiftAnisotropyEnergyCreator | |
| ContactOrderEnergy | |
| ContactOrderEnergyCreator | |
| ContextDependentLRTwoBodyEnergy | |
| ContextDependentOneBodyEnergy | |
| ContextDependentTwoBodyEnergy | |
| ContextIndependentLRTwoBodyEnergy | |
| ContextIndependentOneBodyEnergy | |
| ContextIndependentTwoBodyEnergy | |
| CSD_TorsionEnergy | A knowledge-based torsional potential for small molecules derived from the Cambridge Structural Database by KWK |
| CustomAtomPairEnergy | |
| CustomAtomPairEnergyCreator | |
| DipolarCouplingEnergy | |
| DipolarCouplingEnergyCreator | |
| DirectReadoutEnergy | Implementation of Kono and Sarai's knowledge-based protein-DNA interaction energy |
| DirectReadoutEnergyCreator | |
| 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 |
| DistanceChainbreakEnergyCreator | |
| DNA_BaseEnergy | |
| DNA_BaseEnergyCreator | |
| EnergyMethod | Base class for the energy method hierarchy |
| 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 |
| EnergyMethodOptions | |
| EnergyMethodRegistrator | 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 |
| EnvEnergy | |
| EnvEnergyCreator | |
| EnvSmoothEnergy | |
| EnvSmoothEnergyCreator | |
| Fa_MbenvEnergy | |
| Fa_MbenvEnergyCreator | |
| Fa_MbsolvEnergy | |
| Fa_MbsolvEnergyCreator | |
| FACTSEnergy | |
| GaussianOverlapEnergy | |
| GaussianOverlapEnergyCreator | |
| GenBornEnergy | |
| GenBornEnergyCreator | |
| HybridVDW_Energy | |
| HybridVDW_EnergyCreator | |
| 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 |
| LinearChainbreakEnergyCreator | |
| LK_BallEnergy | |
| LK_BallEnergyCreator | |
| WaterBuilder | |
| LKB_ResidueInfo | |
| LKB_ResiduesInfo | |
| LK_CosThetaEnergy | |
| LK_CosThetaEnergyCreator | |
| LK_SigmoidalFunc | |
| LK_hack | |
| LK_hackCreator | |
| LongRangeTwoBodyEnergy | |
| MembraneCbetaEnergy | |
| MembraneCbetaEnergyCreator | |
| MembraneCenPairEnergy | |
| MembraneCenPairEnergyCreator | |
| MembraneEnvEnergy | |
| MembraneEnvEnergyCreator | |
| MembraneEnvPenalties | |
| MembraneEnvPenaltiesCreator | |
| MembraneEnvSmoothEnergy | |
| MembraneEnvSmoothEnergyCreator | |
| MembraneLipo | |
| MembraneLipoCreator | |
| MetalloPlacementEnergy | |
| MMBondAngleEnergy | |
| MMBondAngleEnergyCreator | |
| MMBondLengthEnergy | |
| MMBondLengthEnergyCreator | |
| MMLJEnergyInter | |
| MMLJEnergyInterCreator | |
| MMLJEnergyIntra | |
| MMLJEnergyIntraCreator | |
| MMTorsionEnergy | |
| MMTorsionEnergyCreator | |
| NMerPSSMEnergy | |
| NMerPSSMEnergyCreator | |
| NMerRefEnergy | |
| NMerRefEnergyCreator | |
| OmegaTetherEnergy | |
| OmegaTetherEnergyCreator | |
| OneBodyEnergy | |
| P_AA_Energy | |
| P_AA_EnergyCreator | |
| P_AA_pp_Energy | |
| P_AA_pp_EnergyCreator | |
| PackStatEnergy | |
| PackStatEnergyCreator | |
| PairEnergy | |
| PairEnergyCreator | |
| 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 |
| PeptideBondEnergyCreator | |
| pHEnergy | |
| pHEnergyCreator | |
| PBLifetimeCache | |
| PoissonBoltzmannEnergy | |
| PoissonBoltzmannEnergyCreator | |
| ProClosureEnergy | |
| ProClosureEnergyCreator | |
| PyContextIndependentOneBodyEnergy | |
| PyContextIndependentTwoBodyEnergy | |
| 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 |
| RamachandranEnergy | |
| RamachandranEnergy2B | |
| RamachandranEnergy2BCreator | |
| RamachandranEnergyCreator | |
| ReferenceEnergy | |
| ReferenceEnergyCreator | |
| ReferenceEnergyNoncanonical | |
| ReferenceEnergyNoncanonicalCreator | |
| ResidualDipolarCouplingEnergy | |
| ResidualDipolarCouplingEnergy_Rohl | |
| ResidualDipolarCouplingEnergy_RohlCreator | |
| ResidualDipolarCouplingEnergyCreator | |
| ResidualDipolarCouplingEnergyRigidSegments | |
| RG_Energy | |
| RG_MinData | |
| RG_Energy_Fast | |
| RG_Energy_FastCreator | |
| RMS_Energy | |
| RMS_EnergyCreator | |
| SA_Energy | |
| SA_EnergyCreator | |
| SecondaryStructureEnergy | |
| SecondaryStructureEnergyCreator | |
| SequenceDependentRefEnergy | |
| SequenceDependentRefEnergyCreator | |
| ShortRangeTwoBodyEnergy | |
| SmoothCenPairEnergy | |
| SmoothCenPairEnergyCreator | |
| SmoothEnvEnergy | |
| SmoothEnvEnergyCreator | |
| SuckerEnergy | |
| SuckerEnergyCreator | |
| SymmetricLigandEnergy | |
| SymmetricLigandEnergyCreator | |
| TwoBodyEnergy | |
| UnfoldedStateEnergy | |
| UnfoldedStateEnergyCreator | |
| VDW_Energy | |
| VDW_EnergyCreator | |
| WaterAdductHBondEnergy | |
| WaterAdductHBondEnergyCreator | |
| WaterAdductIntraEnergy | |
| WaterAdductIntraEnergyCreator | |
| 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 |
| YHHPlanarityEnergy | |
| YHHPlanarityEnergyCreator | |
| mm | |
| mmtrie | |
| MMEnergyTableAtom | |
| MMBondAngleLibrary | |
| MMBondAngleResidueTypeParam | |
| MMBondAngleResidueTypeParamSet | |
| MMBondAngleScore | Calculates scores of mm bond angle paramater sets given an angle |
| MMBondLengthLibrary | |
| MMBondLengthScore | |
| MMLJEnergyTable | Blah |
| MMLJLibrary | A class to maintain a set of MM LJ paramaters |
| 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 |
| MMTorsionLibrary | A class to maintain a set of MM torsion paramaters |
| MMTorsionScore | Calculates scores of mm torsion paramater sets given an angle |
| nv | |
| NVlookup | |
| NVscore | |
| NVscoreCreator | |
| orbitals | |
| OrbitalsAssigned | |
| OrbitalsLookup | |
| OrbitalsScore | |
| OrbitalsScoreCreator | |
| OrbitalsStatistics | |
| packing | |
| Ball | |
| HolesResult | Result class holding the three scores and the per-atom scores |
| HolesEnergy | |
| HolesEnergyCreator | |
| HolesEnergyRes | |
| HolesParams | |
| HolesParamsRes | |
| PoseBalls | |
| PoseBallsLite | |
| SurfVol | |
| SurfVolDeriv | |
| SurfEnergy | |
| SurfEnergyCreator | |
| SurfVolEnergy | |
| SurfVolEnergyCreator | |
| packstat | |
| old | |
| AtomRadiusMap | |
| CavityBall | |
| OrderSphereOnX | |
| OrderSphereOnID | |
| OrderCavBallOnX | |
| OrderCavBallOnRmE | |
| OrderCavBallOnR | |
| OrderCavBallOnRmAnb | |
| SasaResult | |
| SasaOptions | |
| CavityBallCluster | |
| OrderCBC | |
| HTL_EventX | |
| Accumulator | |
| AreaAccumulator | |
| LR_AtomData | |
| PerSphereAccumulator | |
| LR_MP_AtomData | |
| MultiProbePoseAccumulator | |
| MultiProbePerSphereAccumulator | |
| Point | |
| PointPair | |
| Circle | |
| Event | |
| Slice | |
| trace | |
| Array2D | |
| Octree2D | |
| LeeRichards | |
| PackingScoreResData | |
| PackingScore | |
| SimplePDB | |
| SimplePDB_Atom | |
| Sphere | |
| PosePackData | |
| rna | |
| chemical_shift | |
| RNA_ChemicalShiftEnergy | |
| RNA_ChemicalShiftEnergyCreator | |
| ChemicalShiftData | |
| RNA_ChemicalShiftPotential | |
| RNA_CS_residue_parameters | |
| RNA_CS_parameters | |
| Gaussian_parameter | |
| RG_Energy_RNA | |
| RG_Energy_RNACreator | |
| RNA_AtomVDW | |
| RNA_BaseBaseEnergy | |
| Base_pair | |
| Base_stack | |
| RNA_BulgeEnergy | |
| RNA_BulgeEnergyCreator | |
| RNA_CentroidInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| RNA_DataBackboneEnergy | |
| RNA_DataBackboneEnergyCreator | |
| RNA_Datum | |
| RNA_DataInfo | Keep track of RNA centroid information inside the pose |
| RNA_FA_Stack | |
| RNA_FilteredBaseBaseInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| RNA_FittedTorsionInfo | |
| RNA_FullAtomStackingEnergy | |
| RNA_FullAtomStackingEnergyCreator | |
| RNA_FullAtomVDW_BasePhosphate | |
| RNA_FullAtomVDW_BasePhosphateCreator | |
| RNA_LJ_BaseEnergy | |
| RNA_LJ_BaseEnergyCreator | |
| RNA_LowResolutionPotential | |
| RNA_Mg_Energy | |
| RNA_Mg_EnergyCreator | |
| RNA_Mg_KnowledgeBasedPotential | |
| RNA_PairwiseLowResolutionEnergy | |
| RNA_PairwiseLowResolutionEnergyCreator | |
| 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 (!) / |
| RNA_ScoringInfo | Keep track of RNA centroid, useful atom, base-base info inside the pose |
| RNA_SugarCloseEnergy | |
| RNA_SugarCloseEnergyCreator | |
| RNA_TorsionEnergy | |
| RNA_TorsionEnergyCreator | |
| RNA_TorsionPotential | |
| RNA_VDW_Energy | |
| RNA_VDW_EnergyCreator | |
| saxs | |
| DistanceHistogram | |
| FastSAXSEnergy | |
| FastSAXSEnergyCreator | |
| FormFactor | |
| FormFactorManager | Selects a given number of fragments using a quota scheme |
| SAXSEnergy | |
| SAXSEnergyCEN | |
| SAXSEnergyCreator | |
| SAXSEnergyCreatorCEN | |
| SAXSEnergyCreatorFA | |
| SAXSEnergyFA | |
| SinXOverX | |
| sc | |
| _RESULTS | |
| _ATOM_RADIUS | |
| _DOT | |
| _PROBE | |
| Atom | |
| MolecularSurfaceCalculator | |
| ShapeComplementarityCalculator | |
| ShapeComplementarityCalculatorException | |
| solid_surface | |
| SurfaceEnergies | |
| sym_e | |
| symEnergy | |
| symECreator | |
| symmetry | |
| NBListCache | |
| SymmetricEnergies | |
| SymmetricScoreFunction | |
| trie | |
| CPDataCorrespondence | |
| RotamerDescriptor | |
| RotamerDescriptorAtom | |
| RotamerTrie | |
| TrieNode | |
| RotamerTrieBase | |
| TrieCollection | |
| TrieCountPairBase | |
| APBSWrapper | |
| PQR | |
| APBSResult | |
| APBSConfig | |
| I_PARAM | |
| R_PARAM | |
| AtomVDW | |
| CenHBPotential | |
| ChemicalShiftAnisotropy | ChemicalShiftAnisotropys are mainly handled by this class related classed: CSA — a single line in an CSA file - representing a single csa coupling ChemicalShiftAnisotropyEnergy – an energy method which triggers computations handled by this class |
| CSA | |
| ContextGraph | |
| ContextGraphFactory | |
| DenseNeighborIterator | |
| DenseNeighborConstIterator | |
| DenseEnergyContainer | |
| DerivVectorPair | A glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms |
| DipolarCoupling | DipolarCouplings are mainly handled by this class related classed: DC — a single line in an DC file - representing a single dc coupling DipolarCouplingEnergy – an energy method which triggers computations handled by this class |
| DC | |
| DockingScoreFunction | |
| Energies | A cached energies object |
| EnergyNode | |
| EnergyEdge | |
| 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 |
| EMapVector | A vector for storing energy data, initially all values are 0 |
| CenListInfo | Keep track of the cenlist information |
| EnvPairPotential | |
| SelfNeighInfo | |
| FACTSResidueInfo | |
| FACTSPoseInfo | |
| FACTSRotamerSetInfo | |
| FACTSPotential | |
| GenBornResidueInfo | |
| GenBornPoseInfo | |
| GenBornRotamerSetInfo | |
| GenBornPotential | |
| ResidueNeighborIterator | |
| ResidueNeighborConstIterator | |
| LREnergyContainer | |
| Membrane_FAEmbed | |
| Membrane_FAPotential | |
| MembraneEmbed | |
| MembranePotential | |
| MembraneTopology | |
| ResSingleMinimizationData | |
| ResPairMinimizationData | |
| MinimizationNode | |
| MinimizationEdge | |
| 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 |
| MinScoreScoreFunction | |
| AtomNeighbor | Atom-atom neighborlist object |
| NeighborList | |
| OmegaTether | |
| OneToAllNeighborIterator | |
| OneToAllNeighborConstIterator | |
| OneToAllEnergyContainer | |
| P_AA | |
| PairEPotential | |
| PeptideBondedNeighborIterator | |
| PeptideBondedNeighborConstIterator | |
| PeptideBondedEnergyContainer | |
| PoissonBoltzmannPotential | |
| Ramachandran | |
| Ramachandran2B | |
| data_struct | |
| data_structDa | |
| data_structR | |
| data_structDaR | |
| ResidualDipolarCoupling | ResidualDipolarCouplings are mainly handled by this class related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy – an energy method which triggers computations handled by this class |
| RDC | |
| ResidualDipolarCoupling_Rohl | |
| RDC_Rohl | |
| SmallAtNb | |
| ResidueNblistData | |
| ResiduePairNeighborList | |
| Predicate | |
| IsProteinCAPredicate | |
| ResRangePredicate | |
| SelectedResPredicate | |
| ExcludedResPredicate | |
| 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 |
| ScoreFunctionFactory | Collection of functions making a single score_function |
| ScoreFunctionInfo | Info on the scorefunction settings |
| ScoreTypeManager | |
| ScoringManager | |
| DimerPairing | |
| SecondaryStructurePotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| SecondaryStructureWeights | Holds weights and flags for configuring a SecondaryStructureEnergy evaluation |
| SigmoidWeightedCenList | Keep track of the cenlist information stores both centroid counts (T = Real) as well as d_centroid_counts (T = Vector) |
| SmoothScoreTermCoeffs | |
| SmoothEnvPairPotential | |
| BB_Pos | |
| Strands | |
| Helices | |
| SS_Info | |
| Hairpin | |
| Hairpins | |
| SS_Killhairpins_Info | |
| TenANeighborNode | |
| TenANeighborEdge | |
| TenANeighborGraph | |
| TwelveANeighborNode | |
| TwelveANeighborEdge | |
| TwelveANeighborGraph | |
| UnfoldedStatePotential | |
| WaterAdductHBondPotential | |
| sequence | |
| Aligner | |
| AlignerFactory | |
| AnnotatedSequence | |
| SimpleSequenceCreator | |
| SequenceProfileCreator | |
| SequenceCouplingCreator | |
| CompositeSequenceCreator | |
| ChemicalShiftSequenceCreator | |
| CacheableSequenceProfile | |
| ChemicalShiftScoringScheme | |
| ChemicalShiftSequence | |
| CompassScoringScheme | |
| CompositeScoringScheme | |
| CompositeSequence | |
| DerivedSequenceMapping | |
| Cell | |
| DP_Matrix | |
| DPScoringScheme | |
| ExtendAlignerSW | |
| L1ScoringScheme | |
| MatrixScoringScheme | |
| MCAligner | |
| NWAligner | |
| PairScoringScheme | |
| ProfSimScoringScheme | |
| ScoringScheme | |
| ScoringSchemeFactory | |
| Sequence | |
| SequenceAlignment | |
| SequenceAlignmentHasher | |
| SequenceCoupling | |
| SequenceCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| SequenceFactory | |
| SequenceRegistrator | 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 |
| SequenceProfile | |
| SimpleScoringScheme | |
| SWAligner | |
| util | |
| Line | Struct |
| ABEGO | Abego elments |
| ABEGOManager | Manager for abego |
| ChainbreakUtil | |
| numeric | Geometric and mathematical utilities |
| xyzMatrix | |
| xyzVector | |
| ObjexxFCL | C++ headers |
| fmt | |
| protcols | |
| scoring | |
| methods | |
| protocols | The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP |
| abinitio | |
| PcaEvaluator | |
| ShowViolation | |
| ComputeTotalDistCst | |
| Stage1Sampler | |
| AbrelaxApplication | Application level code for Abrelax, Foldconstraints and JumpingFoldconstraints |
| AbrelaxMover | |
| AllResiduesChanged | (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values |
| hConvergenceCheck | |
| ClassicAbinitio | |
| ConstraintFragmentSampler | |
| DomainAssembly | Insert fragments in a linker region. Very similar to what's in looprelax_main |
| DomainAssemblyCreator | |
| DoubleLayerKinematicAbinitio | |
| FoldConstraints | Extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles() |
| FragmentSampler | |
| HedgeArchive | |
| IterativeAbrelax | |
| IterativeBase | |
| IterativeCentroid | |
| IterativeFullatom | |
| JumpingFoldConstraints | |
| KinematicAbinitio | |
| JumpingFoldConstraintsWrapper | |
| KinematicControl | |
| CoordinateConstraintKC | |
| KinematicTaskControl | |
| LoopJumpFoldCst | |
| MembraneAbinitio | |
| PairingStatEntry | |
| _MergableEntries | |
| _HashEntry | |
| PairingStatistics | |
| Protocol | |
| ResolutionSwitcher | |
| AlternativePairings | |
| StrandConstraints | |
| Template | |
| TemplateJumpSetup | |
| FixTemplateJumpSetup | |
| StructureStore | |
| Templates | |
| analysis | |
| InterfaceAnalyzerMover | |
| InterfaceAnalyzerMoverCreator | |
| LoopAnalyzerMover | |
| PackStatMover | |
| anchored_design | |
| Anchor | Anchor class provides for the "anchor" part of a scaffold in anchored interface design |
| AnchoredDesignMover | |
| AnchoredPerturbMover | |
| AnchoredRefineMover | |
| AnchorMoversData | This data class wraps all the data needed for the AnchoredDesign movers |
| antibody | |
| Antibody | Antibody definition |
| AntibodyModeler | |
| CDRH3Modeler | Ab initio modeling of CDR H3 loop |
| GraftMover | Grafts a series of CDR onto a framework |
| GraftOneMover | Grafts only one CDR onto a framework |
| CloseOneMover | Closes only one CDR onto a framework |
| LoopRlxMover | Closes only one CDR onto a framework |
| antibody2 | |
| Ab_TemplateInfo | Antibody2 definition |
| FrameWork | |
| AntibodyInfo | |
| AntibodyModelerProtocol | |
| CDRsMinPackMin | |
| CloseOneCDRLoop | Closes only one CDR onto a framework |
| GraftCDRLoopsProtocol | |
| GraftOneCDRLoop | Grafts only one CDR onto a framework |
| H3CterInsert | H3 CDR, Fragment Insertion and CCD |
| H3PerturbCCD | |
| H3RefineCCD | |
| LHRepulsiveRamp | |
| LHRepulsiveRampLegacy | |
| LHSnugFitLegacy | |
| ModelCDRH3 | Ab initio modeling of CDR H3 loop |
| RefineBetaBarrel | |
| RefineOneCDRLoop | |
| RefineOneCDRLoopCentroid | |
| SnugDock | |
| SnugDockProtocol | |
| backrub | |
| BackrubMover | Class for applying backrub moves to arbitrary protein segments |
| BackrubMoverCreator | |
| BackrubSegment | Class for holind information about individual backrub segments |
| BackrubSidechainMover | |
| BackrubSidechainMoverCreator | |
| boinc | |
| watchdog | |
| Boinc | |
| BoincSharedMemory | |
| BoincCurrentPoseObserver | |
| branch_angle | |
| BranchAngleOptimizer | |
| BranchCoef1 | Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors |
| BranchCoef2 | Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors |
| BranchParam1 | Class to store bond angle energy parameters around a single atom atom with three bonded neighbors |
| BranchParam2 | Class to store bond angle energy parameters around a single atom atom with four bonded neighbors |
| canonical_sampling | |
| mc_convergence_checks | |
| EXCN_Heat_Converged | |
| Heat_ConvergenceCheck | |
| PoolData | |
| HierarchicalLevel | |
| HPool_RMSD | |
| TransferBuffer | |
| MPIBPool_RMSD | |
| MPIHPool_RMSD | |
| MPIPool_RMSD | |
| EXCN_Pool_Converged | |
| Pool_RMSD | |
| Pool_ConvergenceCheck | |
| Pool_Evaluator | |
| DataBuffer | |
| CanonicalSamplingMover | |
| PatchOperation | |
| HamiltonianExchange | |
| HamiltonianExchangeCreator | |
| MetricRecorder | |
| MetricRecorderCreator | |
| MetropolisHastingsMover | |
| MetropolisHastingsMoverCreator | |
| MultiTemperatureTrialCounter | |
| ParallelTempering | |
| ParallelTemperingCreator | |
| PDBTrajectoryRecorder | |
| PDBTrajectoryRecorderCreator | |
| SidechainMetropolisHastingsMover | |
| SidechainMetropolisHastingsMoverCreator | |
| SilentTrajectoryRecorder | |
| SilentTrajectoryRecorderCreator | |
| SimulatedTempering | |
| SimulatedTemperingCreator | |
| TemperatureController | |
| FixedTemperatureController | |
| TemperingBase | |
| ThermodynamicMover | |
| ThermodynamicObserver | |
| TrajectoryRecorder | |
| TrialCounterObserver | |
| TrialCounterObserverCreator | |
| cartesian | |
| CartesianAtom | |
| MD_Bond | |
| MD_Angle | |
| MD_HarmonicDihedral | |
| MolecularDynamics | |
| checkpoint | |
| Timer | : singleton checkpoint timer class |
| FileBuffer | |
| CheckPointer | |
| cluster | |
| Exemplar | Data structure for one similarity measurement (s_ik) for affinity propagation clustering |
| DataPoint | Data structure for one input data point for affinity propagation clustering |
| APCluster | Public interface for doing affinity propagation clustering |
| GatherPosesMover | |
| EnsembleConstraints | |
| EnsembleConstraints_Simple | |
| Cluster | |
| ClusterBase | |
| ClusterPhilStyle | |
| ClusterPhilStyle_Loop | |
| AssignToClustersMover | |
| coarse_rna | |
| CoarseRNA_DeNovoProtocol | The RNA de novo structure modeling protocol |
| SourcePositions | |
| CoarseRNA_Fragments | |
| CoarseRNA_LoopCloser | The RNA de novo structure modeling protocol |
| comparative_modeling | |
| features | |
| ResidueFeature | |
| ResidueFeatureFactory | |
| SSFeature | |
| TorsionFeature | |
| Align_RmsdEvaluator | |
| Align_RotamerEvaluator | |
| AlignmentCluster | |
| AlignmentClustering | |
| AlignmentSet | |
| AlignRmsdTargetEvaluatorCreator | Creator for the AlignRmsdTargetEvaluatorCreator class |
| ExtraThreadingMover | |
| GenericJobInputter | |
| GenericJobInputterCreator | |
| IgnoreSubsetConstraintSet | |
| LoopRelaxMover | |
| LoopRelaxMoverCreator | |
| LoopRelaxThreadingMover | |
| MultiThreadingMover | |
| PartialThreadingMover | |
| RecoverSideChainsMover | |
| StealLigandMover | |
| StealSideChainsMover | |
| ThreadingJob | |
| ThreadingJobInputter | |
| ThreadingJobInputterCreator | |
| ThreadingMover | |
| constraints_additional | |
| BindingSiteConstraintCreator | Mover creator for the BindingSiteConstraint constraint |
| SequenceCoupling1BDConstraintCreator | Mover creator for the SequenceCoupling1BDconstraint |
| SequenceCouplingConstraintCreator | Mover creator for the SequenceCouplingconstraint |
| NamedAtomPairConstraintCreator | This class can be used to replace the standard AtomPairConstraintsCreator; see BrokerMain.cc for an example |
| AmbiguousMultiConstraint | |
| BindingSiteConstraint | |
| CombinedConstraintEvaluator | |
| CombinedConstraintEvaluatorCreator | Creator for the CombinedConstraintsEvaluatorCreator class |
| ConstraintEvaluator | |
| ConstraintEvaluatorCreator | Creator for the ConstraintsEvaluatorCreator class |
| MaxSeqSepConstraintSet | |
| SequenceCoupling1BDConstraint | |
| SequenceCouplingConstraint | |
| contact_map | |
| ContactMap | |
| ContactPartner | Simple class that holds the information on an atom involved in a contact |
| Contact | Simple class representing a contact between two atoms |
| ContactMapCreator | |
| ddg | |
| ddGMover | |
| ddG | |
| ddGData | |
| design_opt | |
| GreedyOptMutationMover | |
| GreedyOptMutationMoverCreator | |
| ParetoOptMutationMover | |
| ParetoOptMutationMoverCreator | |
| PointMutationCalculator | |
| dna | |
| DesignProteinBackboneAroundDNA | |
| DesignProteinBackboneAroundDNACreator | |
| DnaPosition | |
| DnaChains | |
| DnaDesignDef | Command-line dna_defs are of the format "C.501.ADE" they are parsed here into this little class for convenience |
| DnaNeighbor | |
| DnaInterfaceFinder | |
| DnaInterfaceMinMover | |
| DnaInterfaceMinMoverCreator | |
| DnaInterfaceMultiStateDesign | Wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework |
| DnaInterfaceMultiStateDesignCreator | |
| Reversion | |
| ResTypeSequence_lt | |
| DnaInterfacePacker | |
| DnaInterfacePackerCreator | |
| DNABase | |
| DNABasepair | |
| DNABasestep | |
| DNAParameters | |
| PDBOutput | |
| RestrictDesignToProteinDNAInterface | |
| RestrictDesignToProteinDNAInterfaceCreator | |
| RotamerDNAHBondFilter | |
| SeparateDnaFromNonDna | |
| SeparateDnaFromNonDnaCreator | |
| PositionType | Basic struct for remembering position/type information before/during/after design |
| WatsonCrickRotamerCouplings | |
| WatsonCrickRotamerCouplingsCreator | |
| docking | |
| stateless | |
| SaneDockingProtocol | |
| ConformerSwitchMover | This mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction |
| ConformerSwitchMoverCreator | |
| DockingLowResFilter | Low-resolution (centroid-mode) filter for docking. Checks (1) at least some contact is being made between docking partners, (2) clashes are limited so partners are not overlapping and (3) constraints, if present, are met |
| DockingHighResFilter | High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given (2) interface_score must be negative |
| DockingEnsemble | This mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction |
| DockingEnsemblePrepackProtocol | |
| DockingHighRes | |
| DockingHighResLegacy | This mover does the high resolution refinement stage of the RosettaDock algorithm |
| DockingInitialPerturbation | This mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options |
| DockingSlideIntoContact | Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently) |
| FaDockingSlideIntoContact | Slides docking partners together by monitoring fa_rep |
| DockingInitialPerturbationCreator | |
| DockingLowRes | |
| DockingLowResEnsemble | |
| DockingPrepackProtocol | |
| DockingProtocol | This is the standard RosettaDock protocol |
| DockingProtocolCreator | |
| DockMCMCycle | |
| DockMCMProtocol | |
| DockMinMover | |
| DockSetupMover | Allows docking using simulated or parallel tempering |
| DockSetupMoverCreator | |
| DockTaskFactory | |
| RigidBodyInfo | |
| SidechainMinMover | |
| InterfaceSidechainMinMover | |
| TemperedDocking | Allows docking using simulated or parallel tempering |
| TemperedDockingCreator | |
| domain_assembly | |
| AddAssemblyConstraints | |
| AssembleLinkerMover | |
| CombineChainsMover | |
| PostDockAssemblyScorer | |
| electron_density | |
| SetupForDensityScoringMover | |
| SetupForDensityScoringMoverCreator | |
| elscripts | |
| enzdes | |
| enzutil | |
| AddLigandMotifRotamersOperationCreator | |
| AddOrRemoveMatchCsts | A simple wrapper to get the functionality in EnzConstraintIO into mover format |
| AddOrRemoveMatchCstsCreator | |
| AddRigidBodyLigandConfsCreator | |
| BackboneSampler | |
| BackboneSamplerCreator | |
| DesignVsNativeComparison | Class that holds a bunch of native poses and compares them |
| DetectProteinLigandInterfaceOperationCreator | |
| EnzdesBaseProtocol | |
| EnzdesFixBBProtocol | |
| EnzdesFlexBBProtocol | |
| EnzdesFlexibleRegion | |
| EnzdesJobInputter | |
| EnzdesJobInputterCreator | |
| EnzdesJobOutputter | For now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb |
| EnzdesJobOutputterCreator | |
| EnzdesConstraintReporter | |
| PredesignPerturbMover | |
| RepackLigandSiteWithoutLigandMover | Class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues |
| PredesignPerturbMoverCreator | |
| SetCatalyticResPackBehavior | Queries the pose cst cache for the catalytic residues, and sets the behavior for them as specified in the cstfile |
| DetectProteinLigandInterface | Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a packing task to set residues within alpha carbons within cut1 of a ligand (or within cut2 with beta carbons facing inwards) to redesign, and within cut3 (or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided, only do the detection for those residues set to AUTO in the resfile |
| ProteinLigandInterfaceUpweighter | Class to alter a packer task to speficially upweight the protein-ligand interaction energies |
| AddRigidBodyLigandConfs | |
| AddLigandMotifRotamers | |
| DiffAtomSasaFilterCreator | |
| EnzScoreFilterCreator | |
| LigBurialFilterCreator | |
| LigDSasaFilterCreator | |
| LigInterfaceEnergyFilterCreator | |
| RepackWithoutLigandFilterCreator | |
| EnzdesScorefileFilterCreator | |
| LigDSasaFilter | |
| LigBurialFilter | |
| LigInterfaceEnergyFilter | |
| EnzScoreFilter | |
| DiffAtomSasaFilter | |
| RepackWithoutLigandFilter | |
| ValueEvaluator | Tiny helper struct for EnzdesScoreFileFilter |
| EnzdesScorefileFilter | |
| EnzRepackMinimize | |
| EnzRepackMinimizeCreator | |
| ModifyStoredRBConfs | Virtual base class that has some common functionality |
| GenerateStoredRBConfs | Generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used |
| ApplyRandomStoredRBConf | For every ligand that has additional stored rb conformations in the enzdes cacheable observer, the one currently in the pose gets exchanged with a random stored one |
| MinimizeStoredRBConfs | Rotamer trials/minimizes each of the ligand conformations stored in the enzdes cacheable observer and overwrites them with the minimized position. if the new, minimized position is too close to one that already exists, a random small perturbation is applied to ensure diversity note: only jump minimization |
| DiversifyStoredRBConfs | Uses a docking mover to diversiy the stored confs until they're all min_rms_ away from each other note: no scorefunction used here |
| PackRotamersMoverPartGreedy | Mover that packs the side-chains around a given set of target residues in a greedy fashion, and then packs the rest using the sim annealer |
| PackRotamersMoverPartGreedyCreator | |
| ProteinLigandInterfaceUpweighterOperationCreator | |
| SecondaryMatchProtocol | |
| PoseFoundResiduesCombination | Helper class to process and output the different found poses |
| SetCatalyticResPackBehaviorCreator | |
| evaluation | |
| AlignEvaluator | |
| EvaluatorCreator | The Creator class is responsible for creating a particular mover class |
| EvaluatorFactory | Create Evaluator Reporters |
| EvaluatorRegistrator | This templated class will register an instance of an EvaluatorCreator (class T) with the EvaluatorFactory. It will ensure that no EvaluatorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| PCA | |
| SingleValuePoseEvaluator | |
| PoseEvaluator | |
| MetaPoseEvaluator | |
| TimeEvaluator | |
| features | |
| helixAssembly | |
| ConcurrencyTest | |
| ConcurrencyTestCreator | Creator for the HelixBundleFeatures class |
| HelicalFragment | |
| FragmentPair | |
| HelixBundleFeatures | |
| HelixBundleFeaturesCreator | Creator for the HelixBundleFeatures class |
| strand_assembly | |
| StrandBundleFeatures | |
| StrandBundleFeaturesCreator | Creator for the StrandBundleFeatures class |
| StrandFragment | |
| AtomAtomPairFeatures | |
| AtomAtomPairFeaturesCreator | Creator for the AtomAtomPairFeatures class |
| AtomInResidueAtomInResiduePairFeatures | |
| AtomInResidueAtomInResiduePairFeaturesCreator | Creator for the AtomInResidueAtomInResiduePairFeatures class |
| AtomTypesFeatures | |
| AtomTypesFeaturesCreator | Creator for the AtomTypesFeatures class |
| BatchFeatures | |
| BatchFeaturesCreator | Creator for the BatchFeatures class |
| BetaTurnDetectionFeatures | |
| BetaTurnDetectionFeaturesCreator | Creator for the BetaTurnDetectionFeatures class |
| ChargeChargeFeatures | |
| ChargeChargeFeaturesCreator | Creator for the ChargeChargeFeatures class |
| DatabaseFilter | |
| TopCountOfEachInput | |
| TopCountOfAllInputs | |
| TopPercentOfEachInput | |
| TopPercentOfAllInputs | |
| DatabaseJobInputter | |
| DatabaseJobInputterCreator | |
| DatabaseJobOutputter | |
| DatabaseJobOutputterCreator | |
| FeaturesReporter | |
| FeaturesReporterCreator | The Creator class is responsible for creating a particular mover class |
| FeaturesReporterFactory | Create Features Reporters |
| FeaturesReporterRegistrator | This templated class will register an instance of an FeaturesReporterCreator (class T) with the FeaturesReporterFactory. It will ensure that no FeaturesReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| GeometricSolvationFeatures | |
| GeometricSolvationFeaturesCreator | Creator for the GeometricSolvationFeatures class |
| HBondFeatures | |
| HBondFeaturesCreator | Creator for the HBondFeatures class |
| HBondParameterFeatures | |
| HBondParameterFeaturesCreator | Creator for the HBondParameterFeatures class |
| JobDataFeatures | |
| JobDataFeaturesCreator | Creator for the JobDataFeatures class |
| LoopAnchorFeatures | |
| LoopAnchorFeaturesCreator | Creator for the LoopAnchorFeatures class |
| OrbitalsFeatures | |
| OrbitalsFeaturesCreator | Creator for the OrbitalsFeatures class |
| PairFeatures | |
| PairFeaturesCreator | Creator for the PairFeatures class |
| PdbDataFeatures | |
| PdbDataFeaturesCreator | Creator for the PdbDataFeatures class |
| PoseCommentsFeatures | |
| PoseCommentsFeaturesCreator | Creator for the PoseCommentsFeatures class |
| PoseConformationFeatures | |
| PoseConformationFeaturesCreator | Creator for the PoseConformationFeatures class |
| ProteinBackboneAtomAtomPairFeatures | |
| ProteinBackboneAtomAtomPairFeaturesCreator | Creator for the ProteinBackboneAtomAtomPairFeatures class |
| ProteinBackboneTorsionAngleFeatures | |
| ProteinBackboneTorsionAngleFeaturesCreator | Creator for the ProteinBackboneTorsionAngleFeatures class |
| ProteinBondGeometryFeatures | |
| ProteinBondGeometryFeaturesCreator | Creator for the ProteinBondGeometryFeatures class |
| ProteinResidueConformationFeatures | |
| ProteinResidueConformationFeaturesCreator | Creator for the ProteinResidueConformationFeatures class |
| ProteinRMSDFeatures | |
| ProteinRMSDFeaturesCreator | Creator for the ProteinRMSDFeatures class |
| ProteinSilentReport | |
| ProtocolFeatures | |
| ProtocolFeaturesCreator | Creator for the ProtocolFeatures class |
| RadiusOfGyrationFeatures | |
| RadiusOfGyrationFeaturesCreator | Creator for the RadiusOfGyrationFeatures class |
| Report | |
| ReportToDB | |
| ReportToDBCreator | |
| ResidueBurialFeatures | |
| ResidueBurialFeaturesCreator | Creator for the ResidueBurialFeatures class |
| ResidueConformationFeatures | |
| ResidueConformationFeaturesCreator | Creator for the ResidueConformationFeatures class |
| ResidueFeatures | |
| ResidueFeaturesCreator | Creator for the ResidueFeatures class |
| ResidueGridScoresFeatures | |
| ResidueGridScoresFeaturesCreator | Creator for the ResidueGridScoresFeatures class |
| ResidueScoresFeatures | |
| ResidueScoresFeaturesCreator | Creator for the ResidueScoresFeatures class |
| ResidueSecondaryStructureFeatures | |
| ResidueSecondaryStructureFeaturesCreator | Creator for the ResidueSecondaryStructureFeatures class |
| ResidueTotalScoresFeatures | |
| ResidueTotalScoresFeaturesCreator | Creator for the ResidueTotalScoresFeatures class |
| ResidueTypesFeatures | |
| ResidueTypesFeaturesCreator | Creator for the ResidueTypesFeatures class |
| RotamerBoltzmannWeightFeatures | |
| RotamerBoltzmannWeightFeaturesCreator | Creator for the RotamerBoltzmannWeightFeatures class |
| RotamerInitializer | |
| RotamerFeatures | |
| RotamerFeaturesCreator | Creator for the RotamerFeatures class |
| RotamerRecoveryFeatures | |
| RotamerRecoveryFeaturesCreator | Creator for the RotamerRecoveryFeatures class |
| SaltBridgeFeatures | |
| SaltBridgeFeaturesCreator | Creator for the SaltBridgeFeatures class |
| ScoreFunctionFeatures | |
| ScoreFunctionFeaturesCreator | Creator for the ScoreFunctionFeatures class |
| ScoreTypeFeatures | |
| ScoreTypeFeaturesCreator | Creator for the ScoreTypeFeatures class |
| SecondaryStructureSegmentFeatures | |
| SecondaryStructureSegmentFeaturesCreator | Creator for the SecondaryStructureSegmentFeaturesCreator class |
| SecondaryStructureSegment | |
| SmotifFeatures | |
| SmotifFeaturesCreator | Creator for the SmotifFeaturesCreator class |
| StructureFeatures | |
| StructureFeaturesCreator | Creator for the StructureFeatures class |
| StructureScoresFeatures | |
| StructureScoresFeaturesCreator | Creator for the StructureScoresFeatures class |
| UnrecognizedAtomFeatures | |
| UnrecognizedAtomFeaturesCreator | Creator for the UnrecognizedAtomFeatures class |
| fibril | |
| SetupForFibrilMover | |
| filters | |
| sc | |
| TrueFilterCreator | |
| FalseFilterCreator | |
| StochasticFilterCreator | |
| CompoundFilterCreator | |
| CombinedFilterCreator | |
| MoveBeforeFilterCreator | |
| IfThenFilterCreator | |
| TrueFilter | |
| FalseFilter | |
| StochasticFilter | |
| CompoundFilter | Used to define a compound logical statement involving other filters with AND, OR and XOR |
| CombinedFilter | Used to combine multiple seperate filters into a single filter value |
| MoveBeforeFilter | Apply a sub-mover prior to calculating a filter value |
| IfThenFilter | Evaluate to a value contingent on the evaluation of another filter |
| CalculatorFilter | |
| CalculatorFilterCreator | |
| ContingentFilter | |
| ContingentFilterCreator | |
| Filter | |
| FilterCollection | Wrapper-class that contains a vector1 of Filters |
| FilterCreator | Abstract base class for a Filter factory; the Creator class is responsible for creating a particular filter class |
| FilterRegistrator | This templated class will register an instance of an FilterCreator (class T) with the FilterFactory. It will ensure that no FilterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| FilterFactory | |
| HeavyAtomFilter | |
| ReplicateFilter | |
| ReplicateFilterCreator | |
| TimeFilter | |
| TimeFilterCreator | |
| fldsgn | |
| filters | |
| CoreDunbrackFilter | |
| CoreDunbrackFilterCreator | |
| FragQualFilter | |
| FragQualFilterCreator | |
| HelixKinkFilter | |
| HelixKinkFilterCreator | |
| HelixPairingFilter | |
| HelixPairingFilterCreator | |
| HSSTripletFilter | |
| HSSTripletFilterCreator | |
| InterlockingAromaFilter | |
| InterlockingAromaFilterCreator | |
| NcontactsFilter | |
| NcontactsFilterCreator | |
| ParallelBetaPairingPreferenceFilter | |
| ParallelBetaPairingPreferenceFilterCreator | |
| SecondaryStructureFilter | |
| SecondaryStructureFilterCreator | |
| SheetTopologyFilter | |
| SheetTopologyFilterCreator | |
| potentials | |
| sspot | |
| HSPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| NatbiasHelicesSheetPotential | |
| NatbiasHelixPairPotential | |
| NatbiasSecondaryStructureEnergy | NatbiasSecondaryStructureEnergy |
| NatbiasSecondaryStructureEnergyCreator | |
| NatbiasSheetPotential | |
| NatbiasStrandPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| SSPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| AACompositionEnergy | AACompositionEnergy |
| AACompositionEnergyCreator | |
| SetAACompositionPotential | |
| SetAACompositionPotentialCreator | |
| SetSecStructEnergies | |
| SetSecStructEnergiesCreator | |
| topology | |
| BB_Pos | |
| BetaAlphaBetaMotif | |
| BetaAlphaBetaMotifSet | |
| DimerPairing | |
| DimerPairings | |
| HelixPairing | |
| HelixPairingSet | |
| HSSTriplet | |
| HSSTripletSet | |
| Sheet | |
| SheetSet | |
| SheetFoldTypeManager | |
| SS_Base | |
| Strand | |
| Helix | |
| Loop | |
| SS_Info2 | |
| StrandPairing | |
| StrandPairingSet | |
| BluePrintBDR | |
| BluePrintBDRCreator | |
| CircularPermutation | |
| CircularPermutationCreator | |
| MatchResidues | |
| MatchResiduesMover | |
| MatchResiduesMoverCreator | |
| MyAtom | |
| NcontactsCalculator | |
| SheetConstraintsRCG | |
| SheetCstGeneratorCreator | |
| flexpack | |
| annealer | |
| FlexbbSimAnnealer | |
| interaction_graph | |
| FlexbbIGFactory | |
| FlexbbNode | |
| FlexbbEdge | |
| FlexbbInteractionGraph | |
| FlexbbSparseMatrixIndex | |
| MinimalistFlexbbNode | |
| MinimalistFlexbbEdge | |
| MinimalistFlexbbInteractionGraph | |
| OTFFlexbbNode | |
| OTFFlexbbEdge | |
| OTFFlexbbInteractionGraph | |
| PrecomputedFlexbbInteractionGraph | |
| rotamer_set | |
| FlexbbRotamerSet | |
| FlexbbRotamerSets | |
| FlexPacker | |
| OtherContextScoreFunction | |
| flexpep_docking | |
| FlexPepDockingAbInitio | |
| FlexPepDockingFlags | |
| FlexPepDockingLowRes | |
| FlexPepDockingPoseMetrics | |
| FlexPepDockingProtocol | |
| FlexPepDockingProtocolCreator | |
| floppy_tail | |
| FloppyTailMover | FloppyTail mover |
| flxbb | |
| DesignTask | |
| DesignTask_Normal | |
| DesignTask_Layer | |
| FilterStructs | |
| FilterStructs_Packstat | |
| FilterStructs_TotalCharge | |
| FlxbbDesign | |
| FlxbbDesignPack | |
| FlxbbDesignCreator | |
| InterlockAroma | |
| InterlockAromaCreator | |
| LayerDesignOperation | |
| CombinedTaskOperation | |
| LayerDesignOperationCreator | |
| forge | |
| build | |
| BuildInstructionState | |
| SegmentInsertConnectionScheme | |
| Bridge | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| BuildInstruction | Tracks modifications to be made and is capable of making residue length changes on a Pose |
| BuildManager | Container for managing BuildInstructions |
| ConnectRight | Instruction to connect one Pose onto the right side of another |
| GrowLeft | Instruction to create an n-side extension |
| GrowRight | Instruction to create a c-side extension |
| Interval | Simple struct defining a closed interval of residues [left, right] where left <= right |
| RelativeConnectRight | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| RelativeSequencePosition | Computes a position wrt values in given BuildInstruction |
| CountFromLeft | Count starting from interval().left in a BuildInstruction |
| SegmentInsert | Insert an external segment flanked by new regions |
| SegmentRebuild | Instruction to rebuild a segment |
| SegmentSwap | Instruction to swap a segment with an external segment |
| components | |
| VLB_VallMemoryUsage | |
| BDR | |
| BDRSegmentInfo | |
| VarLengthBuild | Component that performs a protocol for user-specified variable length remodeling of protein backbone segments |
| constraints | |
| ConstraintFileCstGeneratorCreator | |
| ConstraintFileRCG | |
| InverseRotamersCstGeneratorCreator | |
| InverseRotamersRCG | RemodelConstraintGenerator that creates AmbiguousConstraints for all positions in a remodeled region towards a list of inverse rotamers. For every remodel position/inverse rotamer pair, there will be one MultiConstraint consisting of three CoordinateConstraints. the three coordinate constraints will be between: 1) remodel res N - invrot N coords 2) remodel res Ca - invrot Ca coords 3) remodel res Cb - invrot Cb coords All of these MultiConstraints are combined to form one AmbiguousConstraint. In effect, this RCG should bias the remodel trajectory such that one remodel residue backbone overlays with one inverse rotamer backbone |
| InvrotTreeCstGeneratorCreator | |
| InvrotTreeRCG | RemodelConstraintGenerator wrapper that makes the constraints generated by an InvrotTree available in VLB or XML |
| NtoC_RCG | |
| NtoCCstGeneratorCreator | |
| RemoveCsts | |
| RemoveCstsCreator | |
| methods | |
| remodel | |
| RemodelAccumulator | |
| RemodelConstraintGenerator | Pure virtual base class |
| LineObject | |
| RemodelData | |
| RemodelDesignMover | |
| RemodelEnzdesCstModule | |
| RemodelLoopMover | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelLoopMoverCreator | |
| RemodelMover | |
| instruction_flags | |
| RemodelMoverCreator | |
| RemodelRotamerLinks | |
| RemodelRotamerLinksCreator | |
| WorkingRemodelSet | |
| Segment | |
| ResidueVicinityCstGeneratorCreator | |
| ResidueVicinityInfo | Small helper class for the ResidueVicinityRCG |
| ResidueVicinityRCG | RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions |
| frag_picker | |
| nonlocal | |
| NonlocalFrags | |
| NonlocalPair | Nonlocal fragment pair |
| quota | |
| ABEGO_SS_Config | Read a config file for quota selector |
| ABEGO_SS_Map | Single pool used by quota selector |
| ABEGO_SS_Pool | Single pool used by quota selector |
| QuotaCollector | A base class for collecting fragments |
| QuotaConfig | Read a config file for quota selector |
| QuotaPool | Single pool used by quota selector |
| quota_limits_sorter_biggest_first | |
| quota_limits_sorter_smallest_first | |
| missing_fraction_sorter_biggest_first | |
| QuotaSelector | Selects a given number of fragments using a quota scheme |
| SecondaryStructurePool | Single pool used by quota selector |
| TorsionBinPool | Single pool used by quota selector |
| scores | |
| ABEGO_SS_Score | |
| MakeABEGO_SS_Score | Maker class that produces a new ABEGO_SS_Score object |
| AdaptiveScoreHistogram | |
| AmbigCSScore | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| MakeAmbigCSScore | Maker class that produces a new AmbigCSScore object |
| AtomBasedConstraintsScore | A base class for all scoring methods that need atom coordinates |
| AtomPairConstraintsScore | Scores a fragment with a set of AtomPair constraints |
| AtomPairConstraintsData | Holds data about a single distance constraint in the form AtomPairConstraintsScore needs |
| MakeAtomPairConstraintsScore | Maker class that produces a new AtomPairConstraintsScore object |
| BFactor | BFactor score counts identical residues |
| MakeBFactor | Maker class that produces a new BFactor object |
| CachingScoringMethod | |
| ConstScore | ConstScore adds a constant to the total score for each position |
| MakeConstScore | Maker class that produces a new ConstScore object |
| CSScore | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| MakeCSScore | Maker class that produces a new CSScore object |
| DihedralConstraintsScore | Scores a fragment with a set of Dihedral constraints |
| MakeDihedralConstraintsScore | Maker class that produces a new DihedralConstraintsScore object |
| DisulfideDistance | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| MakeDisulfideDistance | Matker class that produces a new DisulfideDistance object |
| DisulfideIdentity | DisulfideIdentity score counts identical residues |
| MakeDisulfideIdentity | Maker class that produces a new DisulfideIdentity object |
| FourAtomsConstraintData | Holds data about a single four-body constraint in the form usefull for InterbondAngleScore and DihedralConstraintsScore classes |
| FragmentAllAtomCrmsd | Scores a fragment by its crmsd to the given reference structure |
| MakeFragmentAllAtomCrmsd | Maker class that produces a new FragmentAllAtomCrmsd object |
| FragmentCrmsd | Scores a fragment by its crmsd to the given reference structure |
| MakeFragmentCrmsd | Maker class that produces a new FragmentCrmsd object |
| FragmentCrmsdResDepth | Scores a fragment by its crmsd to the given reference structure |
| MakeFragmentCrmsdResDepth | Maker class that produces a new FragmentCrmsdResDepth object |
| FragmentDME | Scores a fragment by its DME to the given reference structure |
| MakeFragmentDME | Maker class that produces a new FragmentDME object |
| FragmentScoreManager | Holds particular score components, weights and calculates the total score for a fragment candidate |
| FragmentScoreMap | Holds all small scores (score components) for a given fragment |
| FragmentScoringMethod | Fragment candidate score |
| MakeFragmentScoringMethod | Fragment candidate |
| GunnTuple | |
| GunnCost | |
| GunnCostScore | Scores a fragment by its crmsd to the given reference structure |
| MakeGunnCostScore | Maker class that produces a new GunnCostScore object |
| HydrophobicityProfileSimilarity | Scores a fragment by its hydrophobicity similarity |
| MakeHydrophobicityProfileSimilarity | Maker class that produces a new HydrophobicityProfileSimilarity object |
| HydrophobicitySimilarity | Scores a fragment by its hydrophobicity similarity |
| MakeHydrophobicitySimilarity | Maker class that produces a new HydrophobicitySimilarity object |
| InterbondAngleScore | Scores a fragment with a set of Dihedral constraints |
| MakeInterbondAngleScore | Maker class that produces a new InterbondAngleScore object |
| JCoupling | Scores a fragment by the JCouplings |
| MakeJCoupling | Matker class that produces a new JCoupling object |
| LAMBEGO_Similarity | Scores a fragment by torsion bin similarity |
| MakeLAMBEGO_Similarity | Maker class that produces a new TorsionBin object |
| MidPhiOut | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| MakeMidPhiOut | Matker class that produces a new MidPhiOut object |
| MidPsiOut | Scores a fragment by the root mean square deviation of Psi and Psi angles |
| MakeMidPsiOut | Matker class that produces a new MidPsiOut object |
| PartialSecondarySimilarity | Scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster |
| MakePartialSecondarySimilarity | Maker class that produces a new PartialSecondarySimilarity object |
| PCS_FragDistance | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| MakePCS_FragDistance | Matker class that produces a new PCS_FragDistance object |
| Phi | Scores a fragment by its predicted phi similarity |
| MakePhi | Maker class that produces a new Phi object |
| PhiPsiRmsd | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| MakePhiPsiRmsd | Matker class that produces a new PhiPsiRmsd object |
| PhiPsiSquareWell | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| MakePhiPsiSquareWell | Matker class that produces a new PhiPsiSquareWell object |
| ProfileScore | Fragment candidate |
| MakeProfileScore | |
| ProfileScoreBlosum62 | Fragment candidate |
| MakeProfileScoreBlosum62 | |
| ProfileScoreDistWeight | Fragment candidate |
| MakeProfileScoreDistWeight | |
| ProfileScoreL1 | Fragment candidate |
| MakeProfileScoreL1 | |
| ProfileScoreStructL1 | Fragment candidate |
| MakeProfileScoreStructL1 | |
| ProfileScoreSubMatrix | Fragment candidate |
| MakeProfileScoreSubMatrix | |
| ProlinePhiScore | ProlinePhiScore score counts identical residues |
| MakeProlinePhiScore | Maker class that produces a new ProlinePhiScore object |
| Psi | Scores a fragment by its predicted psi similarity |
| MakePsi | Maker class that produces a new Psi object |
| PValuedFragmentScoreManager | Holds particular score components, weights and calculates the total score for a fragment candidate |
| RamaScore | RamaScore score counts identical residues |
| MakeRamaScore | Maker class that produces a new RamaScore object |
| RDCScore | Scores a fragment by its crmsd to the given reference structure |
| MakeRDCScore | Maker class that produces a new RDCScore object |
| ScoreEValuator | Computes E-Value for a Profile object |
| MakeScoreEValuator | |
| SecondaryIdentity | SequenceIdentity score counts how many residues share the same secondary structure |
| MakeSecondaryIdentity | Maker class that produces a new SecondaryIdentity object |
| SecondarySimilarity | Scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster |
| MakeSecondarySimilarity | Maker class that produces a new SecondarySimilarity object |
| SequenceIdentity | SequenceIdentity score counts identical residues |
| MakeSequenceIdentity | Maker class that produces a new SequenceIdentity object |
| SolventAccessibility | Scores a fragment by its predicted solvent accessibility |
| MakeSolventAccessibility | Maker class that produces a new SolventAccessibility object |
| TalosSSSimilarity | Scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster |
| MakeTalosSSSimilarity | Maker class that produces a new TalosSSSimilarity object |
| TorsionBinSimilarity | Scores a fragment by torsion bin similarity |
| MakeTorsionBinSimilarity | Maker class that produces a new TorsionBin object |
| BestTotalScoreSelector | Selects a given number of fragments using a quota scheme |
| BoundedPriorityQueue | |
| BoundedCollector | Keeps the N best fragments candidates for the final selection |
| BoundedCollector_CompareTotalScore | |
| CandidatesCollector | A base class for collecting fragments |
| CompareQueryPosition | Comparator based on a sequence position in a query |
| CompareTotalScore | Comparator based on the total score of fragments |
| CompareByScoreCombination | Comparator based on the linear combination of some score components |
| CompareScoreComponent | Comparator based on one of the score components calculated for fragments |
| CompositeFragmentSelector | Selects fragments by running several selectors |
| Contact | |
| ContactCounts | |
| CS2ndShift | |
| CSTalosIO | |
| CustomScoreSelector | Selects a given number of fragments using a quota scheme |
| DiversifyCrmsdByClustering | Selects fragments by running several selectors |
| DiversifyCrmsdSelector | Selects fragments by running several selectors |
| DiversifyDihedralsSelector | Selects fragments by running several selectors |
| FragmentCandidate | Vector candidate says which X-mer from vall fits to a query sequence |
| FragmentComparatorBase | |
| QuotaDebug | |
| FragmentPicker | The core of the fragment picking machinery |
| FragmentSelectingRule | Selects a given number of fragments just by selecting the best ones |
| GrabAllCollector | Keeps all fragments candidates for the final selection |
| JCouplingIO | |
| LAMBEGO_IO | |
| LazySortedVector1 | |
| PdbIdChunkFilter | |
| AllowPdbIdFilter | Accepts a chunk based on the pdb id of the source protein |
| DenyPdbIdFilter | Denies a chunk based on the pdb id of the source protein |
| PhiPsiTalosIO | |
| SidechainContactDistCutoff | Defines sidechain contact distance cutoffs |
| TorsionBinIO | |
| VallChunk | Chunk of residues extracted from a vall |
| VallChunkFilter | Base class for a chunk filtering mechanism |
| VallProvider | Vector of vall chunks |
| VallResidue | Class for managing a line of the Vall fragment library |
| frags | |
| RMSVallData | |
| TorsionFragment | Class for single piece of torsion fragment |
| SingleResidueTorsionFragmentLibrary | Class for collection of fragments for a single residue position |
| TorsionFragmentLibrary | Class for classic Rosetta fragment library |
| VallData | |
| genetic_algorithm | |
| EntityElement | Entity element |
| EntityElementCreator | Entity element creator |
| EntityElementFactory | Entity element factory |
| EntityElementRegistrator | |
| Entity | |
| Vec1Hash | |
| EntityElementsEqual | |
| EntityRandomizer | |
| DiscreteRandomizer | |
| PositionSpecificRandomizer | Different set of choices at each position in Entity's traits |
| FitnessFunction | |
| GeneticAlgorithm | |
| geometry | |
| grafting | |
| AnchoredGraftMover | Grafting class adapted from Steven Lewis' pose_into_pose algorithm. Basic, and quick, but with many options |
| GraftMoverBase | Base class for GraftMovers. Created for simplicity and control for C++ programmer, as well as PyRosetta user |
| hotspot_hashing | |
| movers | |
| PlaceProbeMover | |
| PlaceSurfaceProbe | |
| PlaceSurfaceProbeCreator | |
| HotspotStub | |
| HotspotStubSet | |
| VectorPair | |
| SearchPattern | |
| ConstPattern | |
| TestPattern | |
| LSMSearchPattern | |
| RotationSearchPattern | |
| SphericalRotationSearchPattern | |
| CartesianSearchPattern | |
| PartitionedSearchPattern | |
| ComposeSearchPatterns | |
| SearchPatternTransform | |
| SearchPatternExpansion | |
| SearchPatternRotSetOp | |
| AddSearchPatternRotSetOp | |
| SICPatternAtTransform | |
| StubGenerator | |
| SurfaceSearchPattern | |
| hybridization | |
| AllResiduesChanged | (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values |
| CartesianHybridize | |
| CartesianSampler | |
| ChunkTrialMover | |
| DDomainParse | |
| DomainAssembly | |
| hConvergenceCheck | |
| FoldTreeHybridize | |
| HybridizeFoldtreeDynamic | |
| HybridizeProtocol | |
| HybridizeProtocolCreator | |
| CartesianSamplerCreator | |
| InsertChunkMover | |
| TemplateHistory | |
| TMalign | |
| WeightedFragmentSmoothTrialMover | |
| WeightedFragmentTrialMover | |
| id | |
| AlignmentID | Unique template identifier class |
| idealize | |
| IdealizeMover | Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points |
| IdealizeMoverCreator | |
| init | |
| inputter | |
| FastaInputter | |
| Inputter | |
| InputterStream | |
| PDBInputter | |
| SilentFileInputter | |
| jd2 | |
| archive | |
| AbstractArchiveBase | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| ArchiveBase | |
| DebugArchive | |
| EXCN_Archive | |
| Batch | Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive |
| ArchiveManager | ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY |
| SortPredicate | |
| EvaluatedArchive | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| MPIArchiveJobDistributor | JobDistributor for the iterative ArchiveManager/Archive Framework |
| CompletionMessage | CompletionMessage(s) are send to the ArchiveManager whenever more than nr_notify decoys have been finished / or when the full batch is finished |
| NormalizedEvaluatedArchive | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| VarianceStatisticsArchive | |
| JobInputterInputSource | |
| parser | |
| BluePrint | |
| DataLoader | A class for loading arbitrary data into the XML parser's DataMap |
| DataLoaderCreator | A class for creating new instances of DataLoaders for use in the XML Parser |
| DataLoaderFactory | A factory for creating DataLoaders, which are able to load arbitrary data into the DataMap used in the XML-based parser. This factory supports the load-time registration scheme allowing DataLoaders to be defined in libraries outside of protocols.lib |
| DataLoaderRegistrator | This templated class will register an instance of an DataLoaderCreator (class T) with the DataLoaderFactory. It will ensure that no DataLoaderCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| FragmentReader | |
| FragSetLoader | A class for loading arbitrary data into the XML parser's DataMap |
| MonteCarloLoader | The MonteCarloLoader will create named MonteCarlo objects and load them into the DataMap |
| ScoreFunctionLoader | A class for loading arbitrary data into the XML parser's DataMap |
| ScoreFunctionLoaderCreator | |
| TaskOperationLoaderCreator | |
| FragSetLoaderCreator | |
| MonteCarloLoaderCreator | |
| TaskOperationLoader | A class for loading arbitrary data into the XML parser's DataMap |
| AtomTreeDiffJobInputter | |
| AtomTreeDiffJobInputterCreator | |
| AtomTreeDiffJobOutputter | |
| AtomTreeDiffJobOutputterCreator | |
| BatchJobInputter | |
| BOINCJobDistributor | |
| DockDesignParser | Reading the xml file and generating the mover |
| FileJobOutputter | |
| FileSystemJobDistributor | |
| InnerJob | |
| InnerMultiThreadingJob | |
| JD2ResourceManager | |
| JD2ResourceManagerCreator | |
| JD2ResourceManagerJobInputter | |
| JD2ResourceManagerJobInputterCreator | |
| Job | |
| JobDistributor | |
| JobDistributorFactory | |
| JobInputter | |
| JobInputterCreator | Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class |
| JobInputterRegistrator | This templated class will register an instance of an JobInputterCreator (class T) with the JobInputterFactory. It will ensure that no JobInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| JobInputterFactory | |
| JobOutputter | |
| JobOutputterCreator | Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class |
| JobOutputterRegistrator | This templated class will register an instance of an JobOutputterCreator (class T) with the JobOutputterFactory. It will ensure that no JobOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| JobOutputterFactory | |
| LazySilentFileJobInputter | |
| LazySilentFileJobInputterCreator | |
| MpiFileBuffer | |
| WriteOut_MpiFileBuffer | |
| DebugOut_MpiFileBuffer | |
| MPIFileBufJobDistributor | |
| MPIMultiCommJobDistributor | |
| MPIWorkPartitionJobDistributor | |
| MPIWorkPoolJobDistributor | |
| MultiThreadingJob | |
| NoOutputJobOutputter | |
| NoOutputJobOutputterCreator | |
| Parser | |
| PDBJobInputter | |
| PDBJobInputterCreator | |
| PDBJobOutputter | |
| PDBJobOutputterCreator | |
| PoseInputStreamJobInputter | |
| PoseInputStreamJobInputterCreator | |
| ScoreMap | |
| ScoreOnlyJobOutputter | |
| ScoreOnlyJobOutputterCreator | |
| ShuffleFileSystemJobDistributor | |
| SilentFileJobInputter | |
| SilentFileJobInputterCreator | |
| SilentFileJobOutputter | |
| CompareTags | |
| SilentFileJobOutputterCreator | |
| SingleFileBuffer | |
| WriteFileSFB | |
| jobdist | |
| BaseJobDistributor | Coordinates processing of jobs across multiple Rosetta processes |
| AtomTreeDiffJobDistributor | Distributor for use with atomtree_diff silent files |
| PlainPdbJobDistributor | Distributor for use with plain old PDB files. Use is strongly discouraged in production environments! |
| PlainRawJobDistributor | Distributor for use with raw files |
| PlainSilentFileJobDistributor | Distributor for use with silent files |
| BasicJob | Each Job object describes a particular input to Rosetta |
| jumping | |
| DisulfTemplate | |
| BaseDisulfPairingLibrary | |
| DisulfPairingLibrary | |
| StandardDisulfPairingLibrary | |
| DisulfPairing | |
| JumpSample | |
| Interval | Two numbers, i.e., jump start end residue, or cut-regions.. |
| BaseJumpSetup | Virtual base class: can create a set of jumps and cuts |
| JumpSetup | |
| JumpDef | |
| JumpsFromAllPairings | |
| JumpSelector | |
| JumpWeightDef | |
| MembraneJump | |
| PairingTemplate | |
| BasePairingLibrary | Returns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors |
| PairingLibrary | |
| SpecificGeometryLibrary | |
| StandardPairingLibrary | |
| RandomSheetBuilder | Select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ |
| ResiduePairJumpSingle | Single residue component of a ResiduePairJump class |
| ResiduePairJump | |
| ResiduePairJumpSetup | |
| JumpDef | |
| SameStrand | 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, |
| SheetBuilder | Select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ |
| kinmatch | |
| KRSQuery | |
| FunGroupTK | |
| BruteFunGroupTK | |
| KinFunGroupTK | |
| ligand_docking | |
| ligand_options | |
| InterfaceInfo | Info for each residue- is it part of the interface and if so, what ligands is it near |
| Interface | For each residue is it in the interface, a mobile region or a non-mobile region? |
| scoring_grid | |
| AddHydrogen | |
| AddHydrogens | |
| AddHydrogensCreator | |
| AtomCountFilter | |
| AtomCountFilterCreator | |
| ChainExistsFilter | |
| ChainExistsFilterCreator | |
| CompleteConnectionsFilter | |
| CompleteConnectionsFilterCreator | |
| CompoundTranslate | |
| CompoundTranslateCreator | |
| DistributionMap | A singleton class that returns a map of strings to enum types |
| FinalMinimizer | |
| FinalMinimizerCreator | |
| GrowLigand | |
| GrowLigandCreator | |
| HBondAcceptorFilter | |
| HBondAcceptorFilterCreator | |
| HBondDonorFilter | |
| HBondDonorFilterCreator | |
| HeavyAtomFilter | |
| HeavyAtomFilterCreator | |
| HighResDocker | |
| HighResDockerCreator | |
| InterfaceBuilder | |
| InterfaceScoreCalculator | |
| InterfaceScoreCalculatorCreator | |
| LigandDockMain | |
| LigandArea | |
| LigandBaseProtocol | Shared functionality for protocols that dock ligands |
| LigandDesign | |
| LigandDesignCreator | |
| InterfaceBuilderLoaderCreator | |
| MoveMapBuilderLoaderCreator | |
| LigandAreaLoaderCreator | |
| InterfaceBuilderLoader | A class for loading InterfaceBuilders into the XML parser's DataMap |
| MoveMapBuilderLoader | A class for loading MoveMapBuilders into the XML parser's DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder |
| LigandAreaLoader | |
| LigandDockProtocol | |
| MinimizeBackbone | |
| MinimizeBackboneCreator | |
| MinimizeLigand | |
| MolarMassFilter | |
| MolarMassFilterCreator | |
| MolecularMassFilter | |
| MolecularMassFilterCreator | |
| MoveMapBuilder | |
| RandomConformerMover | Replace the residue at the given position with a randomly selected conformer from its rotamer library |
| RandomConformers | |
| RandomConformersCreator | |
| ResidueTorsionRestraints | Manages harmonic restraints on torsions, so they can be turned off for packing |
| RigidSearchMover | An optimized mover for Monte Carlo trial of rigid body perturbations |
| Rotate_info | |
| Ligand_info | |
| Rotate | |
| RotateCreator | |
| Rotates | |
| RotatesCreator | |
| SlideTogether | |
| SlideTogetherCreator | |
| StartFrom | |
| StartFromCreator | |
| TetherLigand | |
| Transform_info | |
| Transform | |
| TransformCreator | |
| Translate_info | |
| Translate | |
| TranslateCreator | |
| UnconstrainedTorsionsMover | Juggles torsional constraints with packing or rotamer trials |
| loop_build | |
| LoopBuildMover | |
| LoopMover_SlidingWindow | LoopMover utilizing fragment insertion, ccd loop closure, and minimization |
| LoopMover_SlidingWindowCreator | Creator for the LoopMover_SlidingWindowCreator class |
| loophash | |
| BBExtraData | |
| BBData | |
| BackboneSegment | |
| BackboneDB | |
| EXCN_DB_IO_Failed | |
| EXCN_Invalid_Hashmap | |
| EXCN_No_Extra_Data_To_Write | |
| EXCN_Wrong_DB_Format | |
| EXCN_bbdb_Merge_Failed | |
| FastGapMover | Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much |
| LocalInserter | |
| LocalInserter_SimpleMin | |
| LoopHashDiversifier | |
| LoopHashDiversifierCreator | |
| LoopHashLibrary | |
| LeapIndex | The LeapIndex stores information about a particular Leap. It hold the oroiginal high precision rigid body transform and an Index to a Backbone Database (BackboneDB) that has the actual phi psi angles. THe storage of the precise RT takes a lot of space and may be deprecated at some point, since once it is hashed, it is rarely needed and can be recomputed if it is. Note that the length of the loop is not stored either, this is again done for saving memory, as huge lists of Leaps are typically created all with the same length. THe length is stored and handled by the owner of LeapIndex list. The LeapIndex does not store the actual backbone coordinates of the Leap. It merely contains an index (the BackboneIndex) which refers to a serial store of backbone triples (phi,psi, omega) which are stored somewhere else in a BackboneDB. THis is improtant to save memory storage since multiple Leaps cna share the same backbone triple and redundant storage would be hugely wasteful |
| LegacyLeapIndex | |
| LoopHashMap | Loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates |
| by_index | A functor for sort() |
| LoopHashMoverWrapper | |
| LoopHashMoverWrapperCreator | |
| LoopHashRelaxProtocol | |
| FilterBucket | |
| LoopHashSampler | |
| Mover_LoopHashRefine | |
| MPI_LoopHashRefine | |
| MPI_LoopHashRefine_Emperor | |
| MPI_LoopHashRefine_Master | |
| WorkUnit_LoopHash | |
| loops | |
| loop_closure | |
| ccd | |
| CcdLoopClosureMover | |
| CcdMover | |
| FASelectSlidingWindowLoopClosure | |
| LoopClosure | |
| ShortLoopClosure | |
| SlidingWindowLoopClosure | |
| WidthFirstSlidingWindowLoopClosure | |
| kinematic_closure | |
| KinematicMover | A mover class for performing kinematic loop closure on a peptide segment |
| KinematicPerturber | Pure virtual base class for KinematicPerturber. KinematicPerturbers determine HOW loops should be perturbed. The base class contains a provision for determining WHERE they should be perturbed: MoveMap sensitivity |
| TorsionSamplingKinematicPerturber | Torsion sampling kinematic perturber |
| VicinitySamplingKinematicPerturber | Vicinity sampling kinematic perturber |
| TorsionSweepingKinematicPerturber | WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber |
| NeighborDependentTorsionSamplingKinematicPerturber | Neighbor-dependent torsion sampling kinematic perturber – uses rama2b for phi/psi lookup |
| TorsionRestrictedKinematicPerturber | Torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin) |
| TabooSamplingKinematicPerturber | Taboo-sampling kinematic perturber (still samples randomly, but only within a specific torsion bin, and the Taboo sampler ensures that this torsion bin is varied in each iteration) |
| NeighborDependentTabooSamplingKinematicPerturber | Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b) |
| KinematicWrapper | |
| loop_mover | |
| perturb | |
| LoopMover_Perturb_CCD | |
| LoopMover_Perturb_CCDCreator | Creator for the LoopMover_Perturb_CCDCreator class |
| LoopMover_Perturb_KIC | |
| LoopMover_Perturb_KICCreator | Creator for the LoopMover_Perturb_KICCreator class |
| LoopMover_Perturb_QuickCCD | LoopMover utilizing fragment insertion, ccd loop closure, and minimization |
| LoopMover_Perturb_QuickCCD_Moves | |
| LoopMover_Perturb_QuickCCD_MovesCreator | Creator for the LoopMover_Perturb_QuickCCD_MovesCreator class |
| LoopMover_Perturb_QuickCCDCreator | Creator for the LoopMover_Perturb_QuickCCDCreator class |
| refine | |
| LoopMover_Refine_Backrub | |
| LoopMover_Refine_BackrubCreator | Creator for the LoopMover_Refine_BackrubCreator class |
| LoopMover_Refine_CCD | |
| LoopMover_Refine_CCDCreator | Creator for the LoopMover_Refine_CCDCreator class |
| LoopMover_Refine_KIC | |
| LoopMover_Refine_KICCreator | Creator for the LoopMover_Perturb_KICCreator class |
| LoopRefineInnerCycle | |
| LoopRefineInnerCycleContainer | |
| LoopRefineInnerCycleContainerCreator | Creator for the LoopRefineInnerCycleContainer class |
| LoopRefineInnerCycleFactory | Create LoopMover Reporters |
| RepackTrial | |
| RepackTrialCreator | Creator for the RepackTrial class |
| ShearMinCCDTrial | |
| ShearMinCCDTrialCreator | Creator for the ShearMinCCDTrial class |
| SmallMinCCDTrial | |
| SmallMinCCDTrialCreator | Creator for the SmallMinCCDTrial class |
| IndependentLoopMover | |
| LoopMover | The loop-rebuild protocol |
| loops_definers | |
| LoopsDatabaseDefiner | |
| LoopsDatabaseDefinerCreator | Creator for the LoopsDatabaseDefiner class |
| LoopsDefiner | |
| LoopsDefinerCreator | Creator for the LoopsDefiner class |
| LoopsDefinerFactory | Create LoopsDefiner Reporters |
| LoopsDefinerRegistrator | This templated class will register an instance of an LoopsDefinerCreator (class T) with the LoopsDefinerFactory. It will ensure that no LoopsDefinerCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| LoopsDefinerLoader | A class for loading Loops data into the XML parser's DataMap |
| LoopsDefinerLoaderCreator | |
| LoopsExplicitDefiner | |
| LoopsExplicitDefinerCreator | Creator for the LoopsExplicitDefiner class |
| LoopsFileDefiner | |
| LoopsFileDefinerCreator | Creator for the LoopsFileDefiner class |
| EXCN_Loop_not_closed | |
| FoldTreeFromLoops | |
| FoldTreeFromLoopsCreator | |
| SerializedLoop | Bare-bones representation of a loop |
| Loop | Single loop definition |
| RationalLoopComparator | Orders loops by start position |
| Loop_lt | Used to sort Loops by start-res |
| LoopMoverFactory | Create LoopMover Reporters |
| Loops | |
| LoopsFileFallbackConfiguration | |
| LoopsFileFallbackConfigurationCreator | |
| ResidueIndexDescription | Class which can represent one of many ways in which to describe a particular residue in a pose, and can, when given a pose, find its index. The object should be constructed with all its needed parameters, but, one instance may be copied from another |
| ResidueIndexDescriptionFromFile | |
| LoopFromFileData | |
| LoopsFileData | |
| GuardedLoopsFromFile | This class ensures that the Loops object that is needed to run any of the various forms of loop modeling is correctly initialized from a Pose. If the residues specified from a loops file have not been resolved into the residue indices for a Pose, then this class will die with an assertion failure |
| LoopsFileIO | |
| PoseNumberedLoopFileReader | |
| JSONFormattedLoopsFileReader | |
| LoopsFileLoader | |
| LoopsFileLoaderCreator | |
| LoopsFileOptions | |
| LoopsFileOptionsCreator | |
| MakeRotLib | |
| RotData | |
| match | |
| downstream | |
| ActiveSiteGrid | |
| ClassicMatchAlgorithm | Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner |
| DownstreamAlgorithm | A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits |
| DownstreamBuilder | |
| AtomGeometrySecMatchRPE | Helper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes |
| AtomDistanceSecMatchRPE | RPE to figure out if two atoms are within a given distance atoms need to be set through the parent class add_at_ind function |
| AtomAngleSecMatchRPE | RPE to figure out if three atoms are within a given angle atoms need to be set through the parent class add_at_ind function |
| AtomDihedralSecMatchRPE | RPE to figure out if four atoms are within a given dihedral angle atoms need to be set through the parent class add_at_ind function also checks whether a dihedral is periodic, i.e. multiple minima |
| GeometrySecMatchRPE | Holds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence when an instance of this class is asked to evaluate two residues |
| LigandConformerBuilder | |
| RigidLigandBuilder | |
| ScoringSecMatchRPE | |
| SecMatchEvaluatorFactory | Collection of functions making a single score_function |
| SecMatchResiduePairEvaluator | Base for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue |
| SecondaryMatcherToDownstreamResidue | A class for an algorithm. Given a conformation of the downstream partner, the algorithm is responsible for producing a set of hits |
| hash_upstream_hit | |
| SecondaryMatcherToUpstreamResidue | A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits |
| TargetRotamerCoords | |
| SecondaryMatchUpstreamResProcessor | A simple class to respond to the UpstreamBuilder's process_hit method and pass on the coordinates to its "owning" SecondaryMatcherToUpstreamResidue object |
| us_secmatch_hit_compare | A simple struct to use in list.sort() to ensure that the hits returned by a secondary matcher which has possibly generated upstream hits out-of-order, will return an ordered-hit-list in its build_hits_at_all_positions() method |
| output | |
| DownstreamRMSEvaluator | In the best of all possible worlds, this class would be sufficiently generic such that I could compare RMS for arbitrary subsets of atoms on the downstream partner, but in my first pass implementation, I'm writing while aiming at the RigidLigandBuilder – 1 residue – and I'll compare all heavy atoms |
| LimitHitsPerRotamerFilter | |
| MatchConsolidator | |
| BestMatchesCollection | |
| MatchEvaluator | |
| MatchFilter | |
| StateAccumulatingMatchFilter | |
| MatchGrouper | |
| MatchOutputter | |
| MatchProcessor | |
| OutputWriter | |
| PDBWriter | |
| CloudPDBWriter | Output writer that uses a grouper to group matches and then writes out one pdb file per group, with the different hits from the group in different MODEL sections |
| PoseMatchOutputWriter | Helper class for the MatcherMover that will put a match into a supplied pose |
| PoseInserter | |
| ProcessorFactory | |
| SameChiBinComboGrouper | |
| SameRotamerComboGrouper | |
| SameSequenceGrouper | Class to group matches that represent the same amino acids at the same launch points. E.g. Two matches that both put a cys at launch point #33, a ser a launch point #42 and another ser at launch point #80 would be grouped together – even if they are different rotamers |
| SameSequenceAndDSPositionGrouper | Class that groups based on same sequence and proximity of the downstream object (based on rms ) NOTE: right now only the downstream position according to the first geomcst id upstream residue is taken into account |
| MatchCollisionFilter | |
| UpstreamCollisionFilter | This class is used to detect collisions between the upstream residues and filter out matches that have too much collision. It can perform either hard-sphere collision detection, or score-function (Etable) driven collision detection. Four command-line flags are read by the MatcherTask to initialize this class: match::filter_colliding_upstream_residues match::upstream_residue_collision_tolerance match::upstream_residue_collision_score_cutoff match::upstream_residue_collision_Wfa_atr match::upstream_residue_collision_Wfa_rep match::upstream_residue_collision_Wfa_sol |
| UpstreamDownstreamCollisionFilter | This class is used to detect collisions between upstream residues and downstream poses |
| UpstreamHitCacher | |
| WriteKinemageOutputter | |
| ResidueKinemageWriter | |
| WriteUpstreamCoordinateKinemage | |
| WriteUpstreamHitKinemage | |
| DownstreamCoordinateKinemageWriter | |
| SingleDownstreamResidueWriter | Class for writing conformations of the downstream partner in a kinemage description |
| upstream | |
| ProteinBackboneBuildPoint | |
| OriginalBackboneBuildPoint | |
| ProteinSCSampler | |
| DunbrackSCSampler | Basic class for sidechain sampling that pulls data from the Dunbrack rotamer library. The samples that are returned are the basic rotamers and do not include any expansions by the "ex" flags |
| SampleStrategyData | This class holds all of the data associated with the logic for generating extra samples for a particular chi angle. There are tons of ways concievable to build extra rotamers; the data in this class is intended to group all of that data into one place. This class is not responsible for building extra rotamer samples; that responsibility is given to class FullChiSampleSet |
| BuildSet | A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom |
| FullChiSampleSet | |
| ProteinUpstreamBuilder | |
| ScaffoldBuildPoint | |
| UpstreamBuilder | |
| UpstreamResidueProcessor | |
| UpstreamResTypeGeometry | A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom |
| Bool3DGrid | |
| BumpGrid | |
| Bool3DGridKinemageWriter | |
| Hit | |
| upstream_hit | |
| downstream_hit | |
| match_dspos1 | Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position) |
| Matcher | |
| MatcherOutputStats | |
| MatcherMover | |
| MatcherMoverCreator | |
| MatcherTask | |
| MatchPositionModifier | Base class for objects that modify the match positions based on some criterion |
| SecondaryStructureMPM | Removes positions at which the pose does not have the desired secondary structure |
| NumNeighborsMPM | Removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won't be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward |
| BfactorMPM | Removes positions at which the bfactors for c-alpha atoms are above a desired cutoff. bfactors stored in the pose pdbinfo are taken. if relative bfactors are used, all bfactors are divided by the largest observed bfactor |
| AddAllPositionsMPM | MPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere |
| RemoveNorCTermMPM | Added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching |
| TaskOperationMPM | Mpm that will get a task operation as specified in the tag from the TaskOperationFactory, apply the task operation to the pose and every residue that is then set to designing in the task will be a match position |
| HitHasher | This object hashes hits into 6D voxels. This hash can then be traversed to retrieve the hits that hash to the same voxel (matches!). There are 64 hashes representing the 2^6 ways to perturb the bins in 6D by 1/2 of their bin width |
| HitNeighborFinder | |
| MatchCounter | Class for counting the number of matches given a particular discretization level |
| match_lite_equals | |
| match_lite_hasher | |
| MatchOutputTracker | |
| OccupiedSpaceHash | This class keeps track of the active voxels "up until now" with 64 hashes |
| VoxelSetIterator | Helper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers |
| medal | |
| MedalExchangeMover | |
| MedalMover | |
| motifs | |
| BuildPosition | |
| IRCollection | |
| LigandMotifSearch | |
| Motif | |
| MotifDnaPacker | |
| MotifDnaPackerCreator | |
| MotifHit | |
| MotifLibrary | |
| MotifSearch | |
| SingleMotif | |
| moves | |
| mc_convergence_checks | |
| EXCN_Converged | |
| ConvergenceCheck | |
| _BoolMover | |
| CanonicalSamplingMover | |
| ChangeFoldTreeMover | |
| CompositionMover | |
| CyclicMover | A simple class for cycling between movers in consecutive calls to apply() |
| DataMap | General-purpose store for any reference-count derived object |
| DataMapObj | Templated class to make any data type compatible with ReferenceCounts and OPs. e.g., utility::pointer::owning_ptr< DataMapObj< bool > > stop; You can then place such constructs on the DataMap |
| DsspMover | |
| DsspMoverCreator | |
| FilterMover | |
| IfMover | |
| IfMoverCreator | |
| IteratedConvergenceMover | A mover that repeatedly applies a sub-mover (up to a given maximum) until the given filter returns values within a certain delta for a given number of cycles |
| IteratedConvergenceMoverCreator | |
| JumpOutMover | |
| MonteCarlo | This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics |
| EXCN_Converged | |
| MonteCarloExceptionConverge | |
| Mover | : A mover is an object that can apply a conformational change to a pose |
| MoverContainer | |
| SequenceMover | A Mover that iterates through a vector of Movers, applying each one sequentially |
| RandomMover | RandomMover picks a random move and applies it |
| CycleMover | CycleMover iterates through its vector of Movers one at a time over many calls to apply() |
| RandomMoverCreator | |
| MoverCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| MoverRegistrator | This templated class will register an instance of an MoverCreator (class T) with the MoverFactory. It will ensure that no MoverCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| MoverFactory | |
| MoverStatistics | |
| NullMover | |
| PDBDumpMover | |
| ProfilerMover | |
| MCShowMover | |
| UDPSocketClient | PyMolMover helper class. Handle low level UDP transactions stuff. This is a port of original Python version of UDP socket client written writen for PyRosetta |
| UUID | Unique id of this socket client |
| PyMolMover | |
| PyMolObserver | |
| RampingFunc | |
| LinearFunc | |
| FastLinearFunc | |
| GeometricFunc | Ramps rapidly from the starting value to the final value. Not 1 at x=1. Doesn't really finish at (1,1). func(x) = 1 - exp( -1 * x * inv_xval_at_0p5 * 0.6931 ); |
| InvGeometricFunc | Ramps slowly from the starting value to the final value Non-zero for x = 0. Doesn't really start at (0,0). func(x) = exp( -1 * ( 1 - x ) / ( 1 - xval_at_0p5 ) * 0.6931 ); |
| RampingMover | |
| RampingMoverCreator | |
| RepeatMover | A Mover that repeats an input Mover a user-specified number of times |
| ReplicaExchangeMC | |
| ResId | |
| StructureRestrictor | |
| TrialCounter | |
| MonteCarloUtil | MCResetMover applies a monte carlo reset |
| TrialMover | A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object |
| WhileMover | |
| PoseCondition | |
| mpi | |
| ArchiveMasterBase | |
| multistate_design | |
| MetricCalculatorFitnessFunction | |
| MultiStateAggregateFunction | |
| MultiStateEntity | |
| MultiStateFitnessFunction | |
| PosType | |
| PosTypeCreator | |
| MultiStatePacker | |
| PackingState | |
| PartitionAggregateFunction | |
| SingleState | |
| SingleStateEntityData | |
| SingleStateFitnessFunction | |
| noesy_assign | |
| CovalentCompliance | |
| CrossPeak | |
| Spin | Single dimension of a multidimensional peak, stores putative assignments as indices into Resonance table |
| CrossPeak3D | |
| CrossPeak4D | |
| CrossPeakInfo | Shared information about CrossPeak (one for each proton dimension) |
| CrossPeakList | |
| NoesyModule | |
| DistanceScoreMover | Maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility) |
| EXCN_NoesyAssign | |
| EXCN_UnknownAtomname | |
| EXCN_UnknownResonance | |
| EXCN_AssignmentNotFound | |
| EXCN_FileFormat | |
| FloatingResonance | |
| FoldResonance | |
| FragsToAtomDist | |
| DistanceRecord | |
| MethylNames | |
| MethylNameLibrary | |
| PeakAssignment | Fast access to assignments that are stored in CrossPeak – similar to FragID |
| PeakAssignmentParameters | |
| PeakAssignmentResidueMap | Fast access to assignments by residue number |
| PeakCalibrator | |
| PeakCalibratorMap | |
| PeakFileFormat_Base | |
| PeakFileFormat | |
| PeakFileFormat_xeasy | |
| PeakFileFormat_Sparky | |
| PeakFileFormat_xpk | |
| Resonance | |
| ResonanceList | |
| StructureDependentPeakCalibrator | |
| StructureIndependentPeakCalibrator | |
| nonlocal | |
| BiasedFragmentMover | |
| Chunk | |
| HelixRotate | |
| Policy | |
| PolicyFactory | |
| Region | |
| SheetTranslate | |
| SimpleTreeBuilder | |
| SingleFragmentMover | |
| SingleFragmentMoverCreator | |
| SmoothPolicy | |
| Candidate | |
| StarTreeBuilder | |
| TreeBuilder | |
| TreeBuilderFactory | |
| UniformPolicy | |
| optimize_weights | |
| DDGBindOptEData | |
| DGBindOptEData | Score a "bound" and an "unbound" structure, and minimize the squared error between the difference in their scores and the experimental delta_G of binding |
| ScaleAnnealerTemperatureOperation | |
| IterativeOptEDriver | |
| NestedEnergyTermPNatAAOptEPositionData | |
| NestedEnergyTermDDGMutationOptEData | |
| PNatAAOptERotamerData | |
| PNatRotOptERotamerData | |
| SingleStructureData | |
| OptEPositionData | |
| PNatAAOptEPositionData | |
| PSSMOptEPositionData | |
| PNatRotOptEPositionData | |
| PNatStructureOptEData | |
| DDGMutationOptEData | |
| WeightRangeConstraint | |
| ConstraintedOptimizationWeightFunc | |
| OptEPositionDataFactory | |
| OptEData | |
| OptEMultifunc | OptE mode multifunction class |
| WrapperOptEMultifunc | OptE mode multifunction class |
| OptEVariableExpression | |
| WrappedOptEExpressionCreator | |
| PNatLigPoseOptEData | |
| outputter | |
| FormatStringOutputter | |
| Outputter | |
| PDBOutputter | |
| ResFileOutputter | |
| SilentFileOutputter | |
| pack_daemon | |
| VectorExpression | |
| VariableVectorExpression | |
| IterativeVectorExpression | |
| VectorFunction | |
| VectorFunction2 | |
| VMax | |
| VMin | |
| VMaxBy | Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the largest value in expression 1 |
| VMinBy | Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the smallest value in expression 1 |
| PowExpression | |
| ExpExpression | |
| LnExpression | |
| InSetExpression | Returns "true" if the expression ex evaluates to one of a set of indicated values |
| SurrogateVariableExpression | Stores the result of the surragate expression as if this expression were a variable, but defers to the root expression for questions of deriviatives and which variables are active (this is not a real variable) |
| VectorExpressionCreator | |
| StructureFileNames | |
| DynamicAggregateFunction | |
| EntityFuncExpressionCreator | |
| EntityFunc | |
| EntityCorrespondence | |
| MultistateAggregateFunction | |
| EntityHistoryLT | |
| MultistateFitnessFunction | |
| MPIMultistateFitnessFunction | |
| PackDaemon | |
| DaemonSet | |
| NPDPropCalculator | |
| NPDPropCalculatorCreator | |
| QuickRepacker | |
| BasicSimAnnealerRepacker | |
| RotamerSubsetRepacker | |
| DenseIGRepacker | |
| DoubleDenseIGRepacker | |
| FASTER_IG_Repacker | |
| pb_potential | |
| SetupPoissonBoltzmannPotential | |
| SetupPoissonBoltzmannPotentialCreator | |
| pmut_scan | |
| AlterSpecDisruptionDriver | |
| MutationData | |
| Mutant | |
| PointMutScanDriver | |
| pockets | |
| DarcElectrostaticsBase | |
| DelphiElectrostatics | |
| DarcParticleSwarmMinimizer | |
| spherical_coor_triplet | |
| ray_distance_derivs | |
| FingerprintBase | |
| NonPlaidFingerprint | |
| float4 | |
| PlaidFingerprint | |
| FingerprintMultifunc | Atom tree multifunction class |
| PocketConstraint | This constraint favors creating a pocket suitable for a small-molecule |
| PocketConstraintCreator | Mover creator for the PocketConstraint constraint |
| PCluster | @ |
| Cxyz | |
| PClusterSet | @ |
| PocketGrid | @ |
| EggshellGrid | @ |
| protein_interface_design | |
| filters | |
| AtomicContactCountFilter | |
| AtomicContactCountFilterCreator | |
| AverageDegreeFilter | |
| AverageDegreeFilterCreator | |
| BindingStrainFilter | |
| BindingStrainFilterCreator | |
| BoltzmannFilter | |
| BoltzmannFilterCreator | |
| DesignableResiduesFilter | |
| DesignableResiduesFilterCreator | |
| DisulfideFilter | Filters for structures which could form a disulfide bond across the docking interface |
| DisulfideFilterCreator | |
| FilterScanFilter | |
| FilterScanFilterCreator | |
| HbondsToResidueFilter | Returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class |
| HbondsToResidueFilterCreator | |
| InterfaceHolesFilter | |
| InterfaceHolesFilterCreator | |
| RelativeSegmentFilter | Returns the residues aligned to a segment on the input pdb to the source pdb |
| RelativeSegmentFilterCreator | |
| RmsdFilter | |
| RmsdFilterCreator | |
| SequenceRecoveryFilter | |
| SequenceRecoveryFilterCreator | |
| SpecificResiduesNearInterfaceFilter | |
| SpecificResiduesNearInterfaceFilterCreator | |
| StubScoreFilter | |
| StubScoreFilterCreator | |
| StubScoreLoopsFilter | |
| StubScoreLoopsFilterCreator | |
| Torsion | |
| TorsionCreator | |
| movers | |
| AddChainBreak | Mover that sets a chainbreak in a specified position |
| AddChainBreakCreator | |
| AddSidechainConstraintsToHotspots | |
| AddSidechainConstraintsToHotspotsCreator | |
| BackrubDDMover | |
| BackrubDDMoverCreator | |
| BestHotspotCstMover | Remove all HotspotCst's from the pose except the best X |
| BestHotspotCstMoverCreator | |
| BuildAlaPose | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| BuildAlaPoseCreator | |
| DesignMinimizeHbonds | Used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined |
| DesignMinimizeHbondsCreator | |
| DisulfideMover | |
| DisulfideMoverCreator | |
| DockAndRetrieveSidechains | |
| DockAndRetrieveSidechainsCreator | |
| FavorNativeResiduePreCycle | |
| FavorNativeResiduePreCycleCreator | |
| FavorNonNativeResiduePreCycle | |
| FavorNonNativeResiduePreCycleCreator | |
| HotspotDisjointedFoldTreeMover | |
| HotspotDisjointedFoldTreeMoverCreator | |
| HotspotHasherMover | |
| HotspotHasherMoverCreator | |
| InterfaceRecapitulationMover | Pure virtual base class for movers which redesign and repack the interface |
| InterfaceRecapitulationMoverCreator | |
| LoopFinder | |
| LoopFinderCreator | |
| LoopLengthChange | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| LoopLengthChangeCreator | |
| LoopMoverFromCommandLine | |
| LoopMoverFromCommandLineCreator | |
| LoopOver | Essentially the same as the WhileMover but allows parsing and cloning. Will be removed at a future point. This should now be incorporated into WhileMover |
| LoopOverCreator | |
| LoopRemodel | |
| LoopRemodelCreator | |
| MapHotspot | |
| MapHotspotCreator | |
| NullDesignMover | Does absolutely nothing. useful as if you want to havea final filter without making a move. this can now be assimilated with NullMover |
| PeptideStapleDesignMover | Introduces a peptide staple (ala G. Verdine) to the pose |
| PeptideStapleDesignMoverCreator | |
| PlacementAuctionMover | |
| PlacementAuctionMoverCreator | |
| PlacementMinimizationMover | Simple rb-minimization in a bb-stub constraint biased forcefield. Note that this mover is dependent on a placement mover for setting its stubsets |
| PlacementMinimizationMoverCreator | |
| PlaceOnLoop | |
| PlaceOnLoopCreator | |
| PlaceSimultaneouslyMover | Choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria |
| PlaceSimultaneouslyMoverCreator | |
| PlaceStubMover | Choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria |
| PlaceStubMoverCreator | |
| PrepackMover | |
| PrepackMoverCreator | |
| ProteinInterfaceMultiStateDesignMover | Wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework |
| ProteinInterfaceMultiStateDesignMoverCreator | |
| RandomMutation | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| RandomMutationCreator | |
| RepackMinimize | One round of design/repacking followed by interface sc/bb and rigid-body minimization |
| RepackMinimizeCreator | |
| SaveAndRetrieveSidechains | Saves a pose and reapplies its sequence and rotamers at a later stage. The constructor saves the initial pose, and then any calls to apply replace the residues on the input pose with that saved pose. Notice, that only ALA positions will be replaced, so this is meant to work strictly along with BuildAlaPose moves. This way, if in the design process an interface residue is designed, that will not be reverted to w/t |
| SaveAndRetrieveSidechainsCreator | |
| SetAtomTree | Mover that sets a user-defined atom tree |
| SetAtomTreeCreator | |
| SetTemperatureFactor | Set the temperature (b-)factor column in the PDB according to som filter's value. The filter needs to be ResId-compatible, i.e. to report values on a per-residue basis |
| SetTemperatureFactorCreator | |
| SetupHotspotConstraintsLoopsMover | |
| SetupHotspotConstraintsLoopsMoverCreator | |
| SetupHotspotConstraintsMover | |
| SetupHotspotConstraintsMoverCreator | |
| ShoveResidueMover | |
| ShoveResidueMoverCreator | |
| SpinMover | |
| SpinMoverCreator | |
| BBDofs | |
| ResidueBBDofs | Container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well) |
| Splice | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| SpliceCreator | |
| SpliceSegment | Utility class and functions for dealing with sequence profiles for varying segments in Splice |
| SubroutineMover | |
| SubroutineMoverCreator | |
| TaskAwareCsts | Applies csts (currently only coordinate csts) to every designable position in pose according to taskoperations |
| TaskAwareCstsCreator | |
| TryRotamers | |
| TryRotamersCreator | |
| VLB | User interface for YAB's Variable Length Build |
| VLBCreator | |
| ReportSequenceDifferences | |
| Revert | |
| FavorNativeResidue | |
| FavorNonNativeResidue | |
| DockDesignFilterFactory | |
| ParserJobInputter | |
| ParserJobInputterCreator | |
| Transformation | |
| PatchdockReader | |
| ReportPSSMDifferences | |
| qsar | |
| scoring_grid | |
| AtrGrid | |
| AtrGridCreator | |
| ChargeAtom | Very light representation of an atom that is just a charge and a cartesian space position |
| ChargeGrid | |
| ChargeGridCreator | |
| ClassicGrid | |
| ClassicGridCreator | |
| GridBase | |
| GridCreator | Abstract class fora mover factory. The creator class is responsible for creating a particular mover class |
| GridRegistrator | This templated class will register an instance of a GridCreator (class T) with the GridFactory. It will ensure that no GridCreator is registered twice and centralizes the registration logic |
| GridFactory | |
| GridInitMover | |
| GridInitMoverCreator | |
| GridManager | |
| HbaGrid | |
| HbaGridCreator | |
| HbdGrid | |
| HbdGridCreator | |
| RepGrid | |
| RepGridCreator | |
| ScoringGridLoader | A class for loading ScoringGrids into the XML parser's DataMap |
| ScoringGridLoaderCreator | |
| SingleGrid | |
| SolvationGrid | |
| SolvationGridCreator | |
| SolvationMetaGrid | |
| SolvationMetaGridCreator | |
| VdwGrid | |
| VdwGridCreator | |
| qsarPoint | |
| qsarMap | |
| qsarMover | |
| qsarCreator | |
| qsarOptData | |
| qsarOptFunc | |
| ColorGradient | |
| RenderGridsToKinemage | |
| RenderGridsToKinemageCreator | |
| rbsegment_relax | |
| CCDMoveWrapper | |
| AutoRBMover | |
| FragInsertAndAlignMover | Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply' |
| RBResidueRange | RB residue range |
| RBSegment | Rigid-body segments in a protein |
| RB_lt | |
| RBSegmentMover | Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply' |
| HelicalGaussianMover | |
| SequenceShiftMover | |
| GaussianRBSegmentMover | |
| StrandTwistingMover | |
| RBSegmentRelax | |
| relax | |
| CentroidRelax | Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization |
| parameters | Container for ramp settings |
| ClassicRelaxCreator | |
| ClassicRelax | A functor class which implements the classic Rosetta++ pose_relax protocol |
| SRelaxPose | |
| RelaxScriptCommand | |
| FastRelax | |
| FastRelaxCreator | |
| MiniRelax | |
| RelaxProtocolBase | |
| WorkUnit_BatchRelax | |
| WorkUnit_BatchRelax_and_PostRescore | |
| rigid | |
| MovePoseToMembraneCenterMover | Move pose into a membrane |
| MembraneCenterPerturbationMover | Perturb the pose along membrane normal |
| MembraneNormalPerturbationMover | Rotation pose around membrane center, perturb the membrane normal vector relative to the pose |
| WholeBodyTranslationMover | Translate the whole pose |
| WholeBodyRotationMover | Rotate the whole pose |
| RigidBodyMotionMover | |
| RigidBodyMover | Rigid-body random translate/rotate around centroid of downstream side of a jump |
| RigidBodyPerturbMover | |
| RigidBodyPerturbNoCenterMover | Does a perturbation defined by the rotational and translational magnitudes without setting up the center Can be defined through a move map or with rb_jump Defining through a movemap with multiple jumps leads to a random jump being chosen at apply time, NOT at construction time! This is done to simplify docking with more than one active jump |
| RigidBodyRandomizeMover | |
| RigidBodySpinMover | |
| RigidBodyDeterministicSpinMover | |
| RigidBodyTransMover | |
| UniformSphereTransMover | Rigid-body move that evenly samples the space within a sphere |
| RigidBodyDofRandomizeMover | |
| RigidBodyDofSeqRandomizeMover | |
| RigidBodyDofTransMover | |
| RigidBodyDofSeqTransMover | |
| RigidBodyDofRandomTransMover | |
| RigidBodyDofPerturbMover | Does a perturbation defined by the rotational and translational magnitudes Allowed dofs are specified by a map Can be defined through a move map or with rb_jump. A single jump is selected |
| RigidBodyDofSeqPerturbMover | Does a perturbation defined by the rotational and translational magnitudes Allowed dofs are specified by a map Can be defined through a move map or with rb_jump. All jumps are selected in random order |
| RigidBodyPerturbNoCenterMoverCreator | |
| RollMover | |
| RollMoverCreator | |
| RotateJumpAxisMover | |
| rna | |
| TorsionSet | |
| FragmentLibrary | |
| FullAtomRNA_Fragments | |
| MultipleDomainMover | The RNA de novo structure modeling protocol |
| ChunkSet | |
| RNA_ChunkLibrary | |
| RNA_DataReader | |
| RNA_DeNovoProtocol | The RNA de novo structure modeling protocol |
| RNA_FragmentMover | The RNA de novo structure modeling protocol |
| RNA_Fragments | |
| RNA_HelixAssembler | The RNA de novo structure modeling protocol |
| RNA_IdealCoord | |
| BasePairType | |
| RNA_PairingTemplate | |
| RNA_JumpLibrary | |
| RNA_LoopCloser | The RNA de novo structure modeling protocol |
| RNA_Minimizer | The RNA de novo structure modeling protocol |
| RNA_Relaxer | The RNA de novo structure modeling protocol |
| RNA_SecStructInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| RNA_Pairing | |
| RNA_StructureParameters | |
| suite_info | |
| RNA_suite_list | |
| rosetta_scripts | |
| ParsedProtocol | |
| ParsedProtocolCreator | |
| SavePoseMover | Mover that can be used to save or restore a pose at an arbitrary point during a rosetta scripts protocol. other movers or filters can be set up to access poses saved by this mover during their apply calls |
| SavePoseMoverCreator | |
| rotamer_recovery | |
| RotamerRecovery | |
| RRProtocolCreator | The Creator class is responsible for creating a particular mover class |
| RRProtocolReferenceStructureCreator | |
| RRProtocolRTMinCreator | |
| RRProtocolRotamerTrialsCreator | |
| RRProtocolMinPackCreator | |
| RRProtocolPackRotamersCreator | |
| RRProtocolMoverCreator | |
| RRComparerCreator | The Creator class is responsible for creating a particular mover class |
| RRComparerAutomorphicRMSDCreator | |
| RRComparerRotBinsCreator | |
| RRComparerChiDiffCreator | |
| RRReporterCreator | The Creator class is responsible for creating a particular mover class |
| RRReporterSimpleCreator | |
| RRReporterHumanCreator | |
| RRReporterSQLiteCreator | |
| RotamerRecoveryFactory | Create Rotamer_Recovery Reporters |
| RotamerRecoveryRegistrator | This templated class will register an instance of an RotamerRecoveryCreator (class T) with the RotamerRecoveryFactory. It will ensure that no RotamerRecoveryCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| RotamerRecoveryMover | |
| RotamerRecoveryMoverCreator | |
| RRComparer | The comparison functionality for the rotamer recovery test |
| RRComparerRotBins | |
| RRComparerChiDiff | |
| RRComparerAutomorphicRMSD | |
| RRProtocol | The protocol to run to compute the rotamer recovery the rotamer recovery test |
| RRProtocolMinPack | |
| RRProtocolMover | |
| RRProtocolPackRotamers | |
| RRProtocolReferenceStructure | |
| RRProtocolRotamerTrials | |
| RRProtocolRTMin | |
| RRReporter | The reporting functionality for the rotamer recovery test |
| RRReporterSimple | |
| PerNativeRRReporterHuman | |
| RRReporterHuman | The reporting functionality for the rotamer recovery test in a human readable format |
| RRReporterSQLite | |
| OutputLevel | |
| RotamerDump | |
| RotamerDumpMover | Mover for dumping interaction graph information. The information is appended to the current job |
| sasa_scores | |
| Poly | |
| PPoly | |
| scoring | |
| methods | |
| pcs | |
| GridSearchIterator | |
| PCS_data_per_lanthanides | |
| PCS_data | |
| PCS_Energy | |
| PCS_Energy_parameters_manager | |
| PseudocontactShiftEnergyCreator | |
| PCS_line_data | PCS_line_data class: hold a line of the input file information (.npc format) One PCS_line_data per line in the input file |
| PCS_file_data | PCS_file_data contain all the information of a .npc file one per lanthanide |
| PCS_data_input | PCS_data_input contain all the input information for the PCS. This includes all the information from the .npc files |
| PCS_data_input_manager | |
| PCS_tensor | |
| TensorsOptimizer | |
| pcs2 | |
| GridSearchIterator | |
| GridSearchIteratorCA | |
| PcsDataCenter | |
| PcsDataCenterManager | |
| PcsDataCenterManagerSingleton | |
| PcsDataLanthanide | |
| PcsEnergy | |
| PcsEnergyCreator | |
| PcsEnergyParameter | |
| PcsEnergyParameterManager | |
| PcsGridSearchParameter | |
| PcsGridSearchParameterManager | |
| PcsInputCenter | PcsInputCenter contain all the input information for one paramagnetic center. It can contain multiple data set |
| PcsInputCenterManager | |
| PcsInputFile | PcsInputFile contain all the information of a .npc file one per lanthanide |
| PcsInputLine | PcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file |
| PcsTensor | |
| TensorsOptimizer | |
| TensorsOptimizerFix | |
| TensorsOptimizerSvd | |
| saxs | |
| PDDFEnergy | |
| PDDFEnergyCreator | |
| EnsembleEnergy | |
| EnsembleEnergyCreator | |
| InterchainEnvEnergy | |
| InterchainEnvEnergyCreator | |
| InterchainPairEnergy | |
| InterchainPairEnergyCreator | |
| ResidualDipolarCouplingEnergyRigidSegments | |
| ResidualDipolarCouplingEnergyRigidSegmentsCreator | |
| SpecialRotamerEnergy | |
| SpecialRotamerEnergyCreator | |
| ImplicitFastClashCheck | |
| InterchainPotential | |
| Interface | |
| InterfaceInfo | Keep track of the interface information |
| ResidualDipolarCouplingRigidSegments | ResidualDipolarCouplingRigidSegmentss are mainly handled by this class related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingRigidSegmentsEnergy – an energy method which triggers computations handled by this class |
| seeded_abinitio | |
| CAcstGenerator | |
| CAcstGeneratorCreator | |
| CloseFold | |
| CloseFoldCreator | |
| CoordinateCst | |
| CoordinateCstCreator | |
| DefineMovableLoops | |
| DefineMovableLoopsCreator | |
| GrowPeptides | |
| GrowPeptidesCreator | |
| PlaceFragments | |
| SeedFoldTree | |
| SeedFoldTreeCreator | |
| SeedSetupMover | |
| SeedSetupMoverCreator | |
| SegmentHybridizer | |
| SegmentHybridizerCreator | |
| SwapSegment | |
| SwapSegmentCreator | |
| sic_dock | |
| XfoxmScore | |
| CBScoreVisitor | |
| RigidScore | |
| CBScore | |
| LinkerScore | |
| EdgeStandScore | |
| HelixScore | |
| BuriedPolarScore | |
| JointScore | |
| Rose | |
| CorrectionVisitor | |
| SICFast | |
| Vec3 | |
| xyzStripeHashPose | |
| xyzStripeHashPoseWithMeta | |
| simple_filters | |
| AbinitioBaseFilter | |
| AlaScan | |
| AlaScanFilterCreator | |
| AtomicContactFilter | Detects atomic (<4Ang) contacts between any two atoms of two residues |
| AtomicContactFilterCreator | |
| AtomicDistanceFilter | Detects atomic contacts between two atoms of two residues |
| AtomicDistanceFilterCreator | |
| BatchEvaluator | |
| BatchNrEvaluator | |
| BuriedUnsatHbondFilter | Filters based on an upper bound # of buried unsatisfied polar residues |
| BuriedUnsatHbondFilterCreator | |
| CamShiftEvaluator | |
| CamShiftEvaluatorCreator | Creator for the CamShiftEvaluatorCreator class |
| ChiWellRmsdEvaluator | |
| ChiWellRmsdEvaluatorCreator | Creator for the ChiWellRmsdEvaluatorCreator class |
| PoseMetricEvaluator | |
| COFilter | |
| ConservedPosMutationFilter | |
| ConservedPosMutationFilterCreator | |
| ConstraintScoreCutoffFilter | |
| ConstraintScoreCutoffFilterCreator | |
| ContactMapEvaluator | |
| ContactMapEvaluatorCreator | Creator for the ContactMapEvaluatorCreator class |
| DdgFilter | |
| DdgFilterCreator | |
| DeltaFilter | |
| DeltaFilterCreator | |
| EnergyPerResidueFilter | |
| EnergyPerResidueFilterCreator | |
| EvaluatedTrialMover | |
| ExpiryFilter | |
| ExpiryFilterCreator | |
| ExternalEvaluator | |
| ExtraScoreEvaluatorCreator | Creator for the ExtraScoreEvaluatorCreator class |
| FileExistFilter | |
| FileExistFilterCreator | |
| FileRemoveFilter | |
| FileRemoveFilterCreator | |
| HolesFilter | |
| HolesFilterCreator | |
| InterfaceBindingEnergyDensityFilter | |
| InterfaceBindingEnergyDensityFilterCreator | |
| InterfaceSasaFilter | |
| InterfaceSasaFilterCreator | |
| JScoreEvaluator | |
| JScoreEvaluatorCreator | Creator for the JScoreEvaluatorCreator class |
| JumpEvaluator | |
| JumpNrEvaluator | |
| JumpNrEvaluatorCreator | Creator for the JumpNrEvaluatorCreator class |
| MinValueEvaluator | |
| NativeEvaluatorCreator | Creator for the NativeEvaluatorCreator class |
| NeighborTypeFilter | |
| NeighborTypeFilterCreator | |
| NMerPSSMEnergyFilter | |
| NMerPSSMEnergyFilterCreator | |
| NonSequentialNeighborsFilter | |
| NonSequentialNeighborsFilterCreator | |
| Operator | Simply take a list of filters and combine them using the operation above |
| OperatorFilterCreator | |
| RegionalConnections | |
| PackerNeighborGraphFilter | |
| PackStatFilter | |
| PackStatFilterCreator | |
| PalesEvaluator | |
| PalesEvaluatorCreator | Creator for the PalesEvaluatorCreator class |
| PDDFScoreFilter | |
| PoolEvaluatorCreator | Creator for the PoolEvaluatorCreator class |
| PoseInfoFilter | Detects atomic contacts between two atoms of two residues |
| PoseInfoFilterCreator | |
| PredictedBurialEvaluator | |
| PredictedBurialFnEvaluatorCreator | Creator for the PredictedBurialFnEvaluatorCreator class |
| RangeFilter | |
| RangeFilterCreator | |
| RDC_Evaluator | |
| SelectRDC_Evaluator | |
| RdcEvaluatorCreator | Creator for the RdcEvaluatorCreator class |
| RdcSelectEvaluatorCreator | Creator for the RdcSelectEvaluatorCreator class |
| RdcTargetEvaluatorCreator | Creator for the RdcTargetEvaluatorCreator class |
| RelativePoseFilter | |
| RelativePoseFilterCreator | |
| ReportFilter | |
| ReportFilterCreator | |
| ResidueBurialFilter | |
| ResidueBurialFilterCreator | |
| ResidueCountFilter | |
| ResidueCountFilterCreator | |
| ResidueDistanceFilter | |
| ResidueDistanceFilterCreator | |
| ResidueIEFilter | |
| ResidueIEFilterCreator | |
| ResidueSetChainEnergyFilter | |
| ResidueSetChainEnergyFilterCreator | |
| ResiduesInInterfaceFilter | |
| ResiduesInInterfaceFilterCreator | |
| RGFilter | |
| RmsdEvaluator | |
| SelectRmsdEvaluator | |
| SelectGdtEvaluator | |
| SelectMaxsubEvaluator | |
| SymmetricRmsdEvaluator | |
| LoopRmsdEvaluator | |
| RmsdEvaluatorCreator | Creator for the RmsdEvaluatorCreator class |
| RmsdTargetEvaluatorCreator | Creator for the RmsdTargetEvaluatorCreator class |
| RotamerBoltzmannWeight | |
| RotamerBoltzmannWeightFilterCreator | |
| RPF_ScoreEvaluator | |
| SAXSScoreFilter | |
| ScoreCutoffFilter | |
| ScoreCutoffFilterCreator | |
| ScoreEvaluator | That rewrites the whole pss struct all previous entries will be lost... probably not what one wants.. |
| TruncatedScoreEvaluator | |
| ScoreTypeFilter | |
| ScoreTypeFilterCreator | |
| ShapeComplementarityFilter | |
| ShapeComplementarityFilterCreator | |
| SheetFilter | |
| SidechainRmsdFilter | |
| SidechainRmsdFilterCreator | |
| Sigmoid | Transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset |
| SigmoidFilterCreator | |
| StructuralSimilarityEvaluator | |
| StructureSimilarityEvaluatorCreator | Creator for the StructureSimilarityEvaluatorCreator class |
| Quat | |
| SymmetricMotifFilter | |
| SymmetricMotifFilterCreator | |
| TerminusDistanceFilter | |
| TerminusDistanceFilterCreator | |
| simple_moves | |
| asym_fold_and_dock | |
| AsymFoldandDockMoveRbJumpMover | |
| AsymFoldandDockRbTrialMover | |
| carbohydrates | |
| RingConformationMover | |
| chiral | |
| ChiralMover | |
| hbs | |
| HbsPatcher | |
| oop | |
| OopMover | |
| OopPatcher | |
| OopPuckPlusMover | |
| OopPuckMinusMover | |
| OopDPuckPlusMover | |
| OopDPuckMinusMover | |
| OopRandomPuckMover | |
| OopRandomSmallMover | |
| rational_mc | |
| RationalMonteCarlo | |
| sidechain_moves | |
| JumpRotamerSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| JumpRotamerSidechainMoverCreator | |
| PerturbChiSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| PerturbChiSidechainMoverCreator | |
| PerturbRotamerSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| PerturbRotamerSidechainMoverCreator | |
| SetChiMover | A mover to change one chi angle |
| SetChiMoverCreator | |
| SidechainMCMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| SidechainMCMoverCreator | |
| SidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| SidechainMoverBase | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| SidechainMoverCreator | |
| symmetry | |
| DetectSymmetry | |
| DetectSymmetryMoverCreator | |
| SetupForSymmetryMover | |
| ExtractAsymmetricUnitMover | |
| ExtractAsymmetricPoseMover | |
| SetupForSymmetryMoverCreator | |
| ExtractAsymmetricUnitMoverCreator | |
| ExtractAsymmetricPoseMoverCreator | |
| SetupNCSMover | |
| SetupNCSMoverCreator | |
| SymDockingInitialPerturbation | |
| SymDockingSlideIntoContact | Contrary to the name, slides things apart first, then together |
| FaSymDockingSlideTogether | Slides docking partners together by monitoring fa_rep |
| SymmetrySlider | |
| SequentialSymmetrySlider | |
| OrderedSequentialSymmetrySlider | |
| RandomSymmetrySlider | |
| SymmetricRMSMover | |
| SymMinMover | |
| SymMinMoverCreator | |
| SymPackRotamersMover | |
| SymPackRotamersMoverCreator | |
| SymRotamerTrialsMover | |
| SymEnergyCutRotamerTrialsMover | |
| SymRotamerTrialsMoverCreator | |
| SymShakeStructureMover | |
| AddCavitiesMover | |
| AddConstraintsToCurrentConformationMover | |
| AddConstraintsToCurrentConformationMoverCreator | |
| BackboneMover | |
| SmallMover | A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified |
| ShearMover | A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified |
| SmallMoverCreator | |
| ShearMoverCreator | |
| BBConRotMover | |
| BBGaussianMover | Basic class for implementing Gaussian Perturbation of bb |
| BBG8T3AMover | Particular gaussian mover from the original paper |
| ClearConstraintsMover | |
| ClearConstraintsMoverCreator | |
| ConsensusDesignMover | This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed |
| ConsensusDesignMoverCreator | |
| ConstraintFragmentMover | |
| ConstrainToIdealMover | |
| ConstraintSetMover | |
| ConstraintSetMoverCreator | |
| CutChainMover | Simple mover that sperates Fv from Fl into two seperate chains |
| CutChainMoverCreator | |
| ddG | |
| ddGCreator | |
| DesignRepackMover | Pure virtual base class for movers which redesign and repack the interface |
| DME_FilterMover | |
| DOFHistogramRecorder | |
| DumpPdb | What you think this can now be assimilated into DumpPdbMover |
| DumpPdbCreator | |
| ExtendedPoseMover | |
| ExtendedPoseMoverCreator | |
| FavorSequenceProfile | |
| FavorSequenceProfileCreator | |
| ForceDisulfidesMover | Simple mover that fixes disulfides according to a defined list and then simultaneously repacks within 6A shells around each affected cystein residue |
| ForceDisulfidesMoverCreator | |
| FragmentMover | Abstract base class for FragmentMovers |
| ClassicFragmentMover | A FragmentMover that applies uniform sampling of fragments |
| LoggedFragmentMover | |
| Item | |
| GenericMonteCarloMover | |
| GenericMonteCarloMoverCreator | |
| MinimalRotamer | |
| GroupDiscriminator | Interface class used to break a pose down into a set of component "groups" where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings |
| UserDefinedGroupDiscriminator | |
| ChainGroupDiscriminator | |
| GreenPacker | |
| GunnTuple | |
| GunnCost | |
| HelicalPeptideLengthMover | |
| LoadPDBMover | |
| LoadPDBMoverCreator | |
| LoadUnboundRotMover | |
| LoadUnboundRotMoverCreator | |
| MakePolyXMover | |
| MakePolyXMoverCreator | |
| MembraneTopology | A mover to change one torsion angle |
| MembraneTopologyCreator | |
| MinMover | A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set |
| MinMoverCreator | |
| MinPackMover | Mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing |
| MinPackMoverCreator | |
| MissingDensityToJumpMover | |
| ModifyVariantTypeMover | Adds variant types to selected residues |
| ModifyVariantTypeMoverCreator | |
| MonteCarloRecover | |
| MonteCarloRecoverCreator | |
| MonteCarloTest | |
| MonteCarloTestCreator | |
| MutateResidue | A mover to mutate a single residue |
| MutateResidueCreator | |
| O2M_MutateMover | |
| PackRotamersMover | A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing |
| PackRotamersMoverCreator | |
| PackRotamersMoverLazy | Mover that packs the side-chains using a rotamer library in a lazy fashion |
| PackRotamersMoverLazyCreator | |
| PDBReloadMover | |
| PDBReloadMoverCreator | |
| PeptideStapleMover | |
| ProlineFixMover | |
| RepackSidechainsMover | A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains() |
| RepackSidechainsMoverCreator | |
| RepulsiveOnlyMover | This mover replace designated residues with glycines, and then assigns a "REPLONLY" residue type to those glycines. Those "REPLONLY" residues will make only repulsive contributions to the overall energy |
| ReturnSidechainMover | |
| RotamerTrialsMinMover | |
| EnergyCutRotamerTrialsMinMover | Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant |
| RotamerTrialsMinMoverCreator | |
| RotamerTrialsMover | |
| EnergyCutRotamerTrialsMover | |
| RotamerTrialsMoverCreator | |
| SaneMinMover | |
| SaneMinMoverCreator | |
| ScoreMover | |
| ScoreMoverCreator | |
| SequenceProfileMover | |
| SequenceProfileMoverCreator | |
| SetReturningPackRotamersMover | |
| SetTorsion | A mover to change one torsion angle |
| SetTorsionCreator | |
| ShakeStructureMover | |
| FragmentCost | |
| SmoothFragmentMover | |
| SuperimposeMover | |
| SuperimposeMoverCreator | |
| SwitchChainOrderMover | |
| SwitchChainOrderMoverCreator | |
| SwitchResidueTypeSetMover | A mover that switches a pose between residue type sets (e.g. centroid and fullatom) |
| SwitchResidueTypeSetMoverCreator | |
| SymmetricFragmentMover | A SymmetricFragmentMover that applies uniform sampling of fragments |
| SmoothSymmetricFragmentMover | A SymmetricFragmentMover that applies uniform sampling of fragments |
| TailsScoreMover | |
| TaskAwareMinMover | |
| TaskAwareMinMoverCreator | |
| TorsionDOFMover | TODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code) |
| WobbleMover | A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: -—lfff bbb-— f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl— the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment() |
| sparta | |
| ANN | |
| ChemicalShiftEvaluator | |
| ChemicalShiftEvaluatorCreator | Creator for the ChemicalShiftsEvaluatorCreator class |
| GDB | |
| CORdata | |
| RingData | |
| PDB | |
| Sparta | |
| SpartaLib | { most of the original SPARTA class goes into SpartaLib – to be reused between different evaluators.. |
| star | |
| Extender | |
| StarAbinitio | |
| surface_docking | |
| CentroidRelaxMover | |
| FullatomRelaxMover | |
| SlideIntoSurface | |
| FaSlideIntoSurface | Slides docking partners together by monitoring fa_rep |
| FaSlideAwayFromSurface | Moves the protein away from the surface |
| SurfaceDockingProtocol | |
| SurfaceOrientMover | |
| SurfaceParameters | |
| swa | |
| monte_carlo | |
| RNA_AddMover | |
| RNA_AddOrDeleteMover | |
| RNA_DeleteMover | |
| RNA_O2StarMover | |
| RNA_SWA_MonteCarloMover | |
| RNA_TorsionMover | |
| SubToFullInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| protein | |
| MainChainTorsionSet | |
| StepWiseBetaAntiParallelJumpSampleGenerator | |
| StepWiseProteinCCD_Closer | |
| StepWiseProteinFilterer | |
| StepWiseProteinFragmentSampleGenerator | |
| StepWiseProteinJumpSampleGenerator | |
| StepWiseProteinLoopBridger | |
| StepWiseProteinMainChainSampleGenerator | |
| StepWiseProteinPacker | |
| StepWiseProteinPoseMinimizer | |
| StepWiseProteinPoseSetup | |
| StepWiseProteinResidueSampler | |
| StepWiseProteinScreener | |
| rna | |
| RNA_AnalyticLoopCloser | The RNA de novo structure modeling protocol |
| RNA_LoopCloseSampler | |
| StepWiseRNA_AnalyticalLoopCloseSampler | |
| StepWiseRNA_Base_Sugar_Rotamer | |
| StepWiseRNA_BaseCentroidScreener | |
| Jump_point | |
| pose_data_struct2 | |
| Torsion_Info | |
| output_data_struct | |
| InternalWorkingResidueParameter | |
| SillyCountStruct | |
| SlicedPoseJobParameters | |
| Cluster_Member | |
| StepWiseRNA_Clusterer | |
| Combine_Tags_Info | |
| Filterer_Count | |
| StepWiseRNA_CombineLongLoopFilterer | |
| Anchor_ribose_stub | |
| Euler_angles | |
| Base_bin | |
| compare_base_bin | |
| compare_int_pair | |
| compare_test | |
| StepWiseRNA_JobParameters | |
| StepWiseRNA_JobParameters_Setup | |
| StepWiseRNA_Minimizer | |
| StepWiseRNA_PoseSetup | |
| Residue_info | |
| StepWiseRNA_ResidueSampler | |
| StepWiseRNA_RotamerGenerator | |
| StepWiseRNA_RotamerGenerator_Wrapper | |
| Atom_Bin | |
| VDW_RepScreeninfo | |
| StepWiseRNA_VDW_Bin_Screener | |
| FB_Pose_Data | |
| FloatingBaseChainClosureJobParameter | |
| InputStreamWithResidueInfo | |
| MainChainTorsionSet | |
| PoseFilter | |
| PoseFilter_RMSD_Screen | |
| RigidBodySampler | |
| StepWiseClusterer | |
| StepWiseCombineSampleGenerator | |
| StepWiseDoNothingSampleGenerator | |
| StepWiseFilterer | |
| StepWiseIdentitySampleGenerator | |
| StepWiseJobParameters | |
| StepWisePoseCombineSampleGenerator | |
| StepWisePoseSampleGenerator | |
| StepWisePoseSetup | |
| StepWiseResidueSampler | |
| StepWiseScreener | |
| symmetric_docking | |
| SymDockBaseProtocol | |
| SymDockingHiRes | |
| SymDockingLowRes | |
| SymDockProtocol | |
| SymFoldandDockMoveRbJumpMover | |
| SymFoldandDockRbTrialMover | |
| SymFoldandDockSlideTrialMover | |
| SymRestrictTaskForDocking | |
| SymSidechainMinMover | |
| SymInterfaceSidechainMinMover | |
| toolbox | |
| match_enzdes_util | |
| AlignPoseToInvrotTreeMover | Small mover that takes an invrot tree |
| AllowedSeqposForGeomCst | Simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too |
| EnzConstraintIO | |
| CovalentConnectionReplaceInfo | Helper class to allow for removal of covalent constraints |
| EnzConstraintParameters | Class that holds all the parameters for one specific constraint |
| EnzCstTemplateResAtoms | Helper class for EnzCstTemplateRes, holds atom ids corresponding |
| EnzCstTemplateRes | Helper class for class EnzConstraintParameters, gathers information |
| EnzdesCacheableObserver | |
| EnzdesCstCache | Simple class to store the pose specific enzdes constraint information in the actual pose |
| EnzdesCstParamCache | |
| EnzCstTemplateResCache | |
| ResInteractions | |
| CstResInteractions | |
| EnzdesLoopInfo | |
| EnzdesLoopsFile | Class to process an enzdes loops file |
| EnzdesSeqRecoveryCache | |
| ExternalGeomSampler | The external geom sampler is a class that manages the data necessary to construct the coordinates of the three atoms in the downstream partner |
| InvrotTarget | 'root' target against which the inverse rotamers are built abstract base class to allow for invrots being built against any sort of entity |
| SingleResidueInvrotTarget | |
| InvrotTree | |
| TheozymeInvrotTree | This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile. Shit gets complicated when ambiguous interactions are specified and other residues are interacting (possibly in ambiguous fashion) with these ambiguous residues.. |
| InvrotTreeNode | |
| InvrotCollector | @ brief helper class for collecting all different definitions of invrots from a tree |
| InvrotTreeNodeBase | Abstract base class for an inverse rotamer tree node. Exists so that the target node (InvrotTreeTarget) and the different geom cst nodes (InvrotTreeNode) have a common base class. This is necessary so that a node can point at its parent node in a tree without having to worry about whether that is a target or a regular node |
| LigandConformer | |
| GeomSampleInfo | Class that stores information of one geometric parameter line of the .cst file i.e. angleA or torsionB |
| MatchConstraintFileInfo | |
| MatchConstraintFileInfoList | Simple container class to contain several MatchConstraintFileInfo instances. this can also query the MatchConstraintFileInfos for common upstream restypes and put all their geomsamples into one list |
| pose_manipulation | |
| pose_metric_calculators | |
| BuriedUnsatisfiedPolarsCalculator | |
| CatPiCalculator | |
| ChargeCalculator | |
| ClashCountCalculator | |
| EnergiesData | |
| EmptyVertexData | |
| DecomposeAndReweightEnergiesCalculator | |
| ExplicitWaterUnsatisfiedPolarsCalculator | |
| FragQualCalculator | |
| HPatchCalculator | |
| InterGroupNeighborsCalculator | |
| MetricValueGetter | |
| NeighborhoodByDistanceCalculator | |
| NeighborsByDistanceCalculator | |
| NonlocalContactsCalculator | |
| NumberHBondsCalculator | |
| PackstatCalculator | |
| PiPiCalculator | |
| ResidueDecompositionByChainCalculator | |
| ResidueDecompositionCalculator | |
| RotamerBoltzCalculator | |
| RotamerRecovery | |
| SaltBridgeCalculator | |
| SemiExplicitWaterUnsatisfiedPolarsCalculator | |
| SequenceComparison | |
| SurfaceCalculator | |
| rotamer_set_operations | |
| RigidBodyMoveBaseRSO | |
| RigidBodyMoveRSO | |
| SpecialRotamerRSO | |
| task_operations | |
| DesignAroundOperation | |
| DesignAroundOperationCreator | |
| InterfaceTaskOperation | |
| JointSequenceOperation | |
| JointSequenceOperationCreator | |
| LayerOperations | |
| LimitAromaChi2_RotamerSetOperation | |
| LimitAromaChi2Operation | |
| LimitAromaChi2OperationCreator | |
| ModifyAnnealer | |
| ModifyAnnealerCreator | |
| PreventChainFromRepackingOperation | |
| PreventChainFromRepackingOperationCreator | |
| PreventResiduesFromRepackingOperation | |
| PreventResiduesFromRepackingOperationCreator | |
| ProteinCore | |
| ProteinCoreFilterCreator | |
| ProteinInterfaceDesignOperation | |
| ProteinInterfaceDesignOperationCreator | |
| ReadResfileFromDB | |
| ReadResfileFromDBCreator | |
| RestrictByCalculatorsOperation | |
| RestrictByCalculatorsOperationCreator | |
| RestrictChainToRepackingOperation | |
| RestrictChainToRepackingOperationCreator | |
| RestrictIdentitiesAtAlignedPositionsOperation | |
| RestrictIdentitiesAtAlignedPositionsOperationCreator | |
| RestrictInterGroupVectorOperation | |
| RestrictInterGroupVectorOperationCreator | |
| RestrictNativeResiduesOperation | |
| RestrictNativeResiduesOperationCreator | |
| RestrictNonSurfaceToRepackingOperation | |
| RestrictNonSurfaceToRepackingOperationCreator | |
| RestrictOperationsBase | |
| RestrictResiduesToRepackingOperation | |
| RestrictResiduesToRepackingOperationCreator | |
| RestrictToAlignedSegmentsOperation | |
| RestrictToAlignedSegmentsOperationCreator | |
| RestrictToCDRH3Loop | |
| RestrictToCDRH3LoopCreator | |
| DockingNoRepack1 | |
| DockingNoRepack2 | |
| RestrictToInterface | |
| RestrictToInterfaceCreator | |
| RestrictToInterfaceOperation | |
| RestrictToInterfaceOperationCreator | |
| RestrictToInterfaceVectorOperation | |
| RestrictToInterfaceVectorOperationCreator | |
| RestrictToLoopsAndNeighbors | |
| RestrictToLoopsAndNeighborsCreator | |
| RestrictToNeighborhoodOperation | |
| RestrictToNeighborhoodOperationCreator | |
| RestrictToTerminiOperation | |
| RestrictToTerminiOperationCreator | |
| SelectBySASAOperation | |
| SelectBySASAOperationCreator | |
| SeqprofConsensusOperation | |
| RestrictConservedLowDdgOperation | Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking |
| SeqprofConsensusOperationCreator | |
| RestrictConservedLowDdgOperationCreator | |
| SetIGTypeOperation | |
| SetIGTypeOperationCreator | |
| ThreadSequenceOperation | |
| ThreadSequenceOperationCreator | |
| AllowInsert | |
| ClusterBase | |
| ClusterPhilStyle | |
| ClusterOptions | |
| OP_const_iterator | Const_iterator class for SilentFileData container |
| DecoySetEvaluation | |
| IGLigandDesignEdgeUpweighter | |
| ResidueGroupIGEdgeUpweighter | |
| InteratomicVarianceMatrix | |
| KClusterElement | |
| KClusterData | Database of a K-style Clustering algorithm |
| KCluster | Basic class for performing a K-style Clustering algorithm |
| KMedoid | Typical K-Medoids Clustering Algorithm |
| GreedyKCenter | Greedy K-Center Clustering Algorithm |
| DummyClass | |
| SF_Replica | |
| SelectResiduesByLayer | |
| topology_broker | |
| weights | |
| AbinitioMoverWeight | |
| ConstAbinitioMoverWeight | |
| LargeFragWeight | |
| SmallFragWeight | |
| SmoothFragWeight | |
| AsymFoldandDockClaimer | |
| ClaimerMessage | |
| SuggestValueMessage | |
| ConstraintClaimer | |
| ConstraintEvaluatorWrapper | |
| ConstraintEvaluatorWrapperCreator | Creator for the ConstraintsEvaluatorWrapperCreator class |
| CoordConstraintClaimer | |
| CutBiasClaimer | |
| DensityScoringClaimer | |
| DisulfJumpClaimer | Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore |
| DofClaim | |
| SequenceClaim | |
| BBClaim | |
| JumpClaim | |
| CutClaim | |
| RootClaim | |
| EXCN_TopologyBroker | |
| EXCN_Input | |
| EXCN_Unknown | |
| EXCN_FailedBroking | |
| EXCN_FilterFailed | |
| FibrilModelingClaimer | |
| FoldandDockClaimer | |
| FragmentClaimer | |
| JumpClaimer | Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore |
| LoopFragmentClaimer | |
| MembraneTopologyClaimer | |
| MetalloClaimer | |
| PcsEnergyController | |
| PseudocontactShiftEnergyController | |
| RigidChunkClaimer | Defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers — here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued — in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree |
| CM_SuggestFixResidue | |
| JumpCalculator | Helper class – computes if we have all jupms needed to rigidify the chosen chunk and generate more jumps if needed |
| SequenceClaimer | |
| StartStructClaimer | |
| TemplateFragmentClaimer | Hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates |
| TemplateJumpClaimer | Hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates |
| TopologyBroker | |
| TopologyClaimer | |
| TopologyClaimerFactory | A non-copyable factory for instantiating TopologyClaimers by name. Commonly used TopologyClaimers are registered in the constructor. Additional claimers can be registered after the fact using the add_type() method |
| CmdLineData | |
| ub_e2c | |
| ubi_e2c_modeler | |
| unfolded_state_energy_calculator | |
| UnfoldedStateEnergyCalculatorJobDistributor | |
| UnfoldedStateEnergyCalculatorMover | |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor | |
| viewer | |
| graphics_states_param | |
| ConformationViewer | Observer that attaches to a Conformation and displays graphics |
| GraphicsState | |
| SilentObserver | |
| triangle | |
| triangleIterator | |
| vip | |
| VIP_Mover | |
| VIP_Report | |
| wum | |
| DatabaseEntryWorkUnit | |
| DatabaseQueryWorkUnitManager | |
| MoverList | |
| MPI_Relax | |
| MPI_WorkUnitManager | |
| MPI_WorkUnitManager_Slave | |
| sort_SilentStructOPs | |
| find_SilentStructOPs | This little class is a predicate for finding silent structures in say a vector of silent structures |
| SilentStructStore | |
| WorkUnitBase | The base class for all work units |
| WU_Header | This structure can contain any non-dynamicly allocated data. Any simple data types can be used here, ints, real, floats, char, etc. |
| WorkUnit_Wait | |
| WorkUnit_SilentStructStore | This WorkUnit type has structures in it. Most Workunits should derive from this one rather THe the Base class |
| WorkUnit_MoverWrapper | This WorkUnit type can encapsulate any MoverOP. When registering this WOrkunit provide it with a MoverOP and then, when executed on the slaves, this workunit will run the mover On every single input structure and return the results |
| WorkUnitList | WOrkUnitList is a store for WorkUnitCOPs. THe purpose of this class is to store all the possible WorkUnits that a protocol might need. When needed these are cloned and then used. THis class acts like a library of WorkUnit blueprints |
| WorkUnitQueue | |
| WorkUnitQueue_Swapped | |
| WorkUnitManager | |
| wum2 | |
| EndPoint | |
| StatusResponse | |
| StatusRequest | |
| WorkUnit | The base class for all work units, this is abstract |
| WorkUnit_Wait | WorkUnit that sleeps for X seconds |
| WorkUnit_ElScripts | |
| WUQueue | |
| LoopRebuild | The loop-rebuild protocol |
| LoopRefine | Class LoopRefine for fullatom loop refinement |
| RBSegmentRelaxImpl | |
| utility | Miscellaneous I/O, portability, and algorithmic classes |
| factory | A pluggable class factory system |
| io | File stream I/O classes, primarily for compressed data |
| keys | Keys and key-accessed containers for fast, safe object lookup |
| options | Program options system |
| pointer | |
| access_ptr | |
| owning_ptr | |
| ReferenceCount | |
| ReferenceCountMI | |
| vectorL | |
| vector1 | |
| vector0 | |
| A | |
| A | |
| A | |
| A | Of residues |
| A | |
| Alternating | |
| An | |
| An | |
| BinaryExpression | |
| Computes | |
| CrossoverBehavior | |
| Entry | |
| EXCN_BadInput | |
| EXCN_Msg_Exception | |
| Expression | |
| ExpressionCreator | |
| G | |
| Implements | |
| Implements | |
| Simple | Associates fragment indices with Gunn scores |
| Transformation | |
| Trial | |
| UnaryExpression | |
| VariableExpression | |
| WidgetFactory | |
| WidgetRegistrator |
1.8.4
