| ►Nboost | |
| ►Ncore | A class for reading in the atom type properties |
| ►Nchemical | |
| ►Ncarbohydrates | |
| CCarbohydrateInfo | |
| CCarbohydrateInfoManager | |
| CLinkageConformerData | Holds conformer data for glycan torsional sampling used by the LinkageConformerMover |
| CRootData | |
| CSugarModificationsNomenclatureTableRow | A structure for storing information related to the nomenclature of modified sugars |
| ►Ngasteiger | |
| CGasteigerAtomTypeData | |
| CGasteigerAtomTypeSet | A set of Bcl Atom types |
| CPossibleAtomTypesForAtom | A helper class by which AtomTypes can return all possible atom types for a given atom in a structure that is easily accessed by orbital type |
| ►Nmainchain_potential | |
| CMainchainScoreTable | |
| ►NmmCIF | |
| CmmCIFParser | |
| ►Norbitals | |
| CAssignOrbitals | |
| CICoorOrbitalData | |
| COrbitalType | |
| COrbitalTypeMapper | |
| COrbitalTypeSet | |
| ►Nrings | |
| CRingConformer | A structure for storing information for specific, idealized ring conformers |
| CRingConformerManager | |
| CRingConformerSet | |
| ►Nrna | |
| CGaussianParameter | |
| CRNA_FittedTorsionInfo | |
| CRNA_Info | |
| ►Nrotamers | |
| CBasicRotamerLibrarySpecification | |
| CBasicRotamerLibrarySpecificationCreator | |
| CCenrotRotamerLibrarySpecification | |
| CCenrotRotamerLibrarySpecificationCreator | |
| CDunbrackRotamerLibrarySpecification | |
| CDunbrackRotamerLibrarySpecificationCreator | |
| CNCAARotamerLibrarySpecification | |
| CNCAARotamerLibrarySpecificationCreator | |
| CPDBRotamerLibrarySpecification | |
| CPDBRotamerLibrarySpecificationCreator | |
| CRotamerLibrarySpecification | |
| CRotamerLibrarySpecificationCreator | |
| CRotamerLibrarySpecificationFactory | |
| CRotamerLibrarySpecificationRegistrator | This templated class will register an instance of an RotamerLibrarySpecificationCreator (class T) with the RotamerLibrarySpecificationFactory. It will ensure that no RotamerLibrarySpecification creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CStoredRotamerLibrarySpecification | A class which stores atom coordinates for a rotamer library. Internally, this is stored as a list of name:coordinate maps |
| CStoredRotamerLibrarySpecificationCreator | |
| ►Nsdf | |
| CBondData | |
| CCtabParserBase | |
| CCtabV2000Parser | |
| CCtabV3000Parser | |
| CMolFileIOAtom | |
| CMolFileIOBond | |
| CMolFileIOMolecule | |
| CMolFileIOReader | |
| CMolWriter | |
| CSDFParser | |
| CAcceptorAtomFilter | The filter responsible for obtaining all acceptor atoms |
| CAddAtom | Add an atom to ResidueType |
| CAddAtomAlias | A patch operation for adding an atom alias to a ResidueType |
| CAddBond | Add a bond to ResidueType |
| CAddBondType | A patch operation for adding a specific type of bond to a ResidueType |
| CAddChi | Add a chi angle to ResidueType |
| CAddChiRotamer | Add a rotamer sample to a chi angle of the ResidueType |
| CAddConnect | |
| CAddConnectAndTrackingVirt | Add a connect and tracking virt to the atom |
| CAddConnectDeleteChildProton | Add a connect to the atom, delete child proton |
| CAddProperty | Add a property to ResidueType |
| CAddProtonChi | |
| CAdduct | Description of optional single-atom residue adducts |
| CAPolarHydrogenFilter | The filter responsible for all apolar hydrogens |
| CAppendMainchainAtom | Add a mainchain atom after the last mainchain atom |
| CAromaticAtomFilter | The filter responsible for all aromatic atoms |
| CAtom | |
| CAtomICoor | A basic class containing info of internal coordinates needed for building an atom within a ResidueType |
| CAtomProperties | |
| CAtomPropertiesManager | |
| CAtomType | Basic atom type |
| CAtomTypeDatabaseIO | |
| CAtomTypeSet | Set of AtomTypes |
| CAutomorphismIterator | Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations |
| CBond | Basic chemical Bond |
| CCacheableResidueTypeSets | A (Pose-cacheable) container for ResidueTypeSets |
| CChangeAncestory | |
| CChangeBondType | A patch operation for changing the bond type of a given bond |
| CChemicalManager | Class managing different sets of atom_type_set and residue_type_set |
| CChiralFlipAtoms | Execute chiral flip (primarily: at CA) |
| CChiralFlipNaming | Execute chiral flip (primarily: at CA) |
| CClearChiRotamers | A patch operation for clearing all rotamer bins from the chi of a ResidueType |
| CConnectSulfurAndMakeVirtualProton | Add a connection to the residue's sulfur and make a virtual proton to track the position of the connection atom |
| CCopyEdge | |
| CCopyVertex | |
| CDeleteActCoordAtom | Delete an act coord atom Added by Andrew M. Watkins in April 2015 |
| CDeleteAtom | Delete an atom |
| CDeleteChildProton | Delete child proton |
| CDeleteMetalbindingAtom | Delete a metal binding atom Added by Andrew M. Watkins in April 2015 |
| CDeleteProperty | 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) Rewritten by Vikram K. Mulligan on 25 Aug. 2016 to use enums wherever possible for speed |
| CDeleteTerminalChi | Delete terminal chi angle Added by Andrew M. Watkins in April 2015 |
| CDeleteVariantType | A patch operation for deleting a VariantType from a ResidueType |
| CElectronConfiguration | Describes the electron configuration of atoms |
| CElement | Stores element properties |
| CElementSet | A set of Bcl Elements |
| CGlobalResidueTypeSet | A collection of ResidueType defined |
| CGraphvizPropertyWriter | Callback class for write_graphviz - outputs properties for the nodes and edges |
| CHeavyAtomFilter | The filter responsible for obtaining all heavy atoms |
| CHeavyAtomWithHydrogensFilter | The filter responsible for finding heavy atoms with hydrogens |
| CHeavyAtomWithPolarHydrogensFilter | The filter responsible for obtaining all heavy atoms with polar hydrogens attached to them |
| CHydrogenAtomFilter | The filter responsible for all hydrogens |
| CICoorAtomID | Atom 's ID in internal coordinates in a ResidueType |
| CIdealBondLengthSet | A set of Elements |
| CMergeBehaviorManager | |
| CMetapatch | A class patching basic ResidueType to create variant types, containing multiple PatchCase |
| CMMAtomType | Basic MM atom type |
| CMMAtomTypeSet | A set of MMAtomTypes |
| CMutableChiRecord | A class containing bundled info about chis |
| CMutableICoorRecord | A basic class containing basic info of internal coordinates needed for building an atom within a ResidueType This is a simplified representation, used for MutableResidueType. It contains all the information, but is intended to be somewhat easier to update for added/deleted atoms than the standard AtomICoor |
| CMutableResidueConnection | A simple class marking atoms at inter-residue connections |
| CMutableResidueType | A class for defining a type of residue, modifiable version |
| CNCAARotLibBBTorsions | Set the mainchain torsion indices that a noncanonical rotamer library depends upon |
| CNCAARotLibNumRotamerBins | Set the number of rotamer bins per chi for an NCAA that is not in dunbrack |
| CNCAARotLibPath | Set the path to a rotamer library for an NCAA that is not in dunbrack |
| COrbital | Basic chemical atom |
| CPatch | A class patching basic ResidueType to create variant types, containing multiple PatchCase |
| CPatchCase | A single case of a patch, eg proline Nterminus is a case of NtermProteinFull |
| CPatchOperation | A single operation that needs to be applied in a residue patch |
| CPolarHydrogenFilter | The filter responsible for all polar hydrogens |
| CPoseResidueTypeSet | A ResidueTypeSet which can be cached in the Pose |
| CPrependMainchainAtom | Add a mainchain atom before the first mainchain atom |
| CRamaPreproFilename | Set the filenames for RamaPrePro scoring tables |
| CRamaPreproResname | Set the residue name for RamaPrePro scoring tables |
| CRealFilter | A filtered graph that doesn't contain fake/virtual atoms and fake/virtual bonds |
| CRedefineChi | Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTMs |
| CRemoveRotamerSpecifications | Remove existing rotamer specifications (of any type) |
| CRenameAtom | Rename atom |
| CReplaceMainchainAtom | Replace a mainchain atom |
| CReplaceProtonWithBromine | Replace proton with bromine |
| CReplaceProtonWithChlorine | Replace proton with chlorine |
| CReplaceProtonWithEthyl | Replace proton with ethyl |
| CReplaceProtonWithFluorine | Replace proton with fluorine |
| CReplaceProtonWithHydroxyl | Replace proton with hydroxyl |
| CReplaceProtonWithIodine | Replace proton with iodine |
| CReplaceProtonWithMethoxy | Replace proton with methoxy |
| CReplaceProtonWithMethyl | Replace proton with methyl |
| CReplaceProtonWithTrifluoromethyl | Replace proton with trifluoromethyl |
| CRerootEdgeSorter | Edge sorting: Return true if we should prefer edge1 over edge2 |
| CRerootRestypeVisitor | |
| CResConnID | 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 |
| CResetBondLength | A patch operation for resetting the length of a bond within a ResidueType |
| CResidueConnection | A simple class marking atoms at inter-residue connections |
| CResidueDatabaseIO | |
| CResidueProperties | |
| CResidueType | A class for defining a type of residue |
| CResidueTypeBase | A base class for definiting types of residues |
| CResidueTypeFinder | |
| CResidueTypeKinWriter | |
| CResidueTypeSelector | A class picking out a subset of ResidueType by multiple criteria |
| CResidueTypeSelectorSingle | A base class for defining a ResidueTypeSelector by a single criterion |
| CResidueTypeSet | An abstract interface to a set of ResidueTypes |
| CResidueTypeSetCache | |
| CRestypeDestructionEvent | Special signal that the ResidueType is getting destroyed |
| CRigidDistanceVisitor | Utility visitor for find_nbr_dist Will only traverse those atoms in the "rigid" portion of graph around the starting atom. "Rigid" includes direct neighbors and atoms connected by non-rotatable bonds e.g. all rings, all double/triple bonds, methyl groups, single atoms, etc |
| CSelector_AA | Does the residue belong to ANY of these AAs? |
| CSelector_BASENAME | Does the residue have to ANY of these basenames? |
| CSelector_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 |
| CSelector_HAS_ATOMS | Does the residue have ALL of the listed atoms?: |
| CSelector_MATCH_VARIANTS | Does the residue have ALL of the variant types and no more |
| CSelector_NAME1 | Does the residue belong to ANY of these one-letter codes? |
| CSelector_NAME3 | Does the residue have ANY of these three-letter codes? |
| CSelector_NO_VARIANTS | Does the residue have NO variant types? |
| CSelector_PROPERTY | Does the residue have ANY of these properties? |
| CSelector_UPPER_ATOM | Does the main chain of this residue follow from the given position label? |
| CSelector_VARIANT_TYPE | Does the residue have ANY of variant types? |
| CSet_AA | Set residue's aa |
| CSetAllAtomsRepulsive | Set the residue neighbor radius |
| CSetAtomicCharge | Set an atom's charge |
| CSetAtomType | Set atom's chemical type |
| CSetBackboneHeavyatom | Set an atom as backbone heavy atom |
| CSetDisulfideAtomName | Set an atom as this residue's disulfide forming atom |
| CSetFormalCharge | A patch operation for setting the formal charge of a ResidueType's atom |
| CSetICoor | Set an atom's AtomICoord |
| CSetInterchangeabilityGroup_String | Set the interchangeability_group string for a ResidueType |
| CSetIO_String | Set residue's name1 and name3 |
| CSetMMAtomType | Set atom's MM chemical type |
| CSetNbrAtom | Set the residue neighbor atom |
| CSetNbrRadius | Set the residue neighbor radius |
| CSetNetFormalCharge | A patch operation for setting the net formal charge of a whole ResidueType |
| CSetOrientAtom | Set orient atom selection mode |
| CSetPolymerConnectAtom | Set an atom as polymer connection |
| CSetVirtualShadow | Set virtual shadow atoms |
| CVDDistanceMatrix | Utility class for VD-indexed matrix |
| CVirtualizeAll | Virtualize all |
| CVirtualizeSidechain | Virtualize sidechain |
| ►Nconformation | |
| ►Ncarbohydrates | |
| CGlycanNode | Class to store info a node (residue) within a glycan tree |
| CGlycanTree | Class to store info a glycan tree |
| CGlycanTreeSet | Class to store info on all glycan trees of a pose |
| CGlycanTreeSetObserver | The CacheablePoseObserver version of GlycanTreeSet that will react to pose length changes. |
| ►Nmembrane | |
| CAqueousPoreParameters | A class for defining an aqueous pore |
| CEXCN_Illegal_Arguments | |
| CEXCN_Membrane | Parent Exception - Exception Membrane |
| CEXCN_Membrane_Bounds | Membrane Out of Bounds Exception |
| CEXCN_MembraneFoldTree | Fold tree Exception for membrane proteins |
| CEXCN_NonMembrane | Non Membrane Pose Exception |
| CEXCN_Resource_Definition | Resource Manager Exception |
| CEXCN_VirtualRsd | Virtual Residue Definition Exception |
| CImplicitLipidInfo | Definition of an implicit membrane with parameters for different lipid compositions |
| CMembraneInfo | Data describing the relationship between protein(s) and a membrane environment |
| CSpan | |
| CSpanningTopology | |
| ►Norbitals | |
| COrbitalXYZCoords | |
| ►Nparametric | |
| CBooleanValuedParameter | BooleanValuedParameter class, used to store a single Boolean-valued parameter for parametric backbone generation |
| CParameter | Parameter class, used to store a single parameter for parametric backbone generation |
| CParameterizationCalculatorProperties | |
| CParameters | Parameters class, used to store sets of parameters for parametric backbone generation |
| CParametersSet | ParametersSet class, used to store sets of parameters for parametric backbone generation |
| CParametrizationCalculator | ParametrizationCalculator class, used for parametric backbone generation |
| CRealValuedParameter | RealValuedParameter class, used to store a single real-valued parameter for parametric backbone generation |
| CRealVectorValuedParameter | RealVectorValuedParameter class, used to store a single vector-valued parameter for parametric backbone generation |
| CSizeValuedParameter | SizeValuedParameter class, used to store a single core::Size-valued parameter for parametric backbone generation |
| CSizeVectorValuedParameter | SizeVectorValuedParameter class, used to store a single utility::vector1<core::Size>-valued parameter for parametric backbone generation |
| ►Nsignals | |
| CConnectionEvent | Signal a change in the connection with a Conformation object, e.g. destruction or transfer |
| CGeneralEvent | Signals a general change in a Conformation |
| CIdentityEvent | Signals a change in residue identity in a Conformation |
| CLengthEvent | Signals a change in length of residues in a Conformation |
| CXYZEvent | Signals a change in XYZ coordinates in a Conformation |
| ►Nsymmetry | |
| CMirrorSymmetricConformation | Mirror symmetric conformation contains the same symminfo logic, but also includes special logic for mirror symmetries |
| CSymDof | |
| CSymmData | |
| CSymmDataLoader | |
| CSymmDataLoaderCreator | |
| CSymmetricConformation | A symmetric conformation: has an additional data member "SymmetryInfo" class |
| CSymmetryInfo | |
| CSymmetryTransform | |
| CSymSlideInfo | |
| CVirtualCoordinate | |
| CAbstractRotamerTrie | |
| CAddEdgeVisitor | |
| CAtom | |
| CAtomGraphEdgeData | |
| CAtomGraphVertexData | |
| CConformation | A container of Residues and the kinematics to manage them |
| CConformationKinWriter | |
| CDefaultCubeHash | Uses default boost::hash combine to hash Cubes |
| CExactResidueMatcher | |
| CPointGraphEdgeData | |
| CPointGraphVertexData | |
| CPseudoBond | |
| CPseudoBondCollection | |
| CResidue | Instance Residue class, used for placed residues and rotamers |
| CResidueFactory | Collection of functions making a single residue |
| CResidueKinWriter | |
| CResidueMatcher | |
| CRotamerSetBase | |
| CUltraLightResidue | |
| CWatsonCrickResidueMatcher | |
| ►Nenergy_methods | |
| CDEEREnergy | |
| CDEEREnergyCreator | |
| ►Nenvironment | |
| CDofPassport | |
| CEnvCore | |
| CEXCN_Env_Exception | |
| CEXCN_FTSketchGraph | |
| ►CFoldTreeSketch | |
| CNode | |
| CLengthChecker | |
| CLocalPosition | |
| CSequenceAnnotation | |
| ►Nenzymes | |
| CEnzymeData | A structure for storing reaction information for specific virtual enzymes |
| CEnzymeManager | |
| ►Nfragment | |
| ►Npicking_old | |
| ►Nconcepts | |
| CBook | Forward declaration for Book |
| CBook_VallResidues | |
| CExtent | Forward declaration for Extent |
| CLibrarian | Forward declaration for core::fragment::picking_old::concepts::Librarian |
| CLibrarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary | |
| CLibrary | Forward declaration for Library |
| CLibrary_VallSections | |
| ►Nvall | |
| ►Neval | |
| CABEGOEval | Scores a fragment based on sum of secondary structure identity and sequence identity |
| CEnergyEval | Scores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction |
| CIdentityEval | Scores a fragment based on sum of secondary structure identity and sequence identity |
| CVallFragmentEval | Base class for Vall ExtentEvaluator |
| ►Ngen | |
| CLengthGen | Default constant length fragment Vall ExtentGenerator |
| CSecStructGen | Generator that requires fragments to have a specific secondary structure string |
| CVallFragmentGen | Base class Vall ExtentGenerator |
| ►Nscores | |
| CVallFragmentScore | Base Vall FragmentScore struct |
| CVallLibrarian | Librarian that picks fragments from the Vall |
| CVallLibrary | Vall fragment library |
| CVallResidue | Class for managing a line of the Vall fragment library |
| CVallResidues | Wrapper for a collection of VallResidue |
| CVallSection | Class implementing the Book concept for a continuous section of lines in the Vall library |
| CVallSections | Wrapper for a collection of VallSection |
| CFragmentLibraryManager | Singleton class for accessing fragment libraries |
| ►Nrna | |
| CFragmentLibrary | |
| CFullAtomRNA_Fragments | |
| CRNA_FragmentHomologyExclusion | |
| CRNA_Fragments | |
| CTorsionSet | |
| CAnnotatedFragData | FragData that contains additional information |
| CBaseCacheUnit | |
| CBBTorsionAndAnglesSRFD | |
| CBBTorsionSRFD | |
| CCacheWrapper | |
| CConstantLengthFragSet | A set of fragments that contains fragments of a constant length read in from a fragment file |
| CConstantLengthFragSetIterator_ | |
| CConstFrameIterator | |
| CDownJumpSRFD | |
| CFragCache | |
| CFragData | |
| CFragFactory | |
| CFragID | |
| CFragID_Iterator | |
| CFragmentIO | |
| CFragmentRmsd | |
| CFragmentSetLoader | FragmentSetLoader constructs a FragSet instance from data provided by the ResourceManager |
| CFragmentSetLoaderCreator | FragmentSetLoaderCreator allows the ResourceLoaderFactory to create a FragmentSetLoader instance, which in turn can load a FragmentSet |
| CFragSet | The FragSet: (Interface Definition – Virtual BaseClass ) |
| CFragSetCollection | |
| CFragStore | |
| CFrame | 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 |
| CFrameIterator | |
| CFrameIteratorWorker_ | |
| CFrameList | |
| CFrameListIterator_ | |
| CIndependentBBTorsionSRFD | 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) |
| CJumpingFrame | 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 |
| CMapCacheUnit | |
| CMinimalFragSet | |
| CMinimalFragSetIterator_ | |
| CNonContinuousFrame | 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! |
| COrderedFragSet | |
| COrderedFragSetIterator_ | |
| CSecondaryStructure | 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, |
| CSecstructSRFD | |
| CSingleResidueFragData | 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 |
| Ctorsions | |
| CUpJumpSRFD | |
| CVectorCacheUnit | |
| ►Ngrid | |
| CCartGrid | |
| ►Nid | |
| CAtomID | Atom identifier class. Defined by the atom number and the residue number |
| CAtomID_Map | Map from Atom identifiers to contained values class |
| CAtomID_Map_AtomID | |
| CAtomID_Map_bool | |
| CAtomID_Map_Real | |
| CBondID | Two more classes, temporary for testing purposes |
| CCacheableAtomID_MapVector | AtomID_Map< xyzVector< Real > > |
| CDOF_ID | Kinematics DOF identifier class |
| CDOF_ID_Map | Map from Atom DOF identifiers to contained values class |
| CDOF_ID_Range | Kinematics DOF identifier (with range) class |
| CEXCN_AtomNotFound | |
| CJumpID | |
| CNamedAtomID | Atom identifier class |
| CNamedAtomID_Map | Map from Atom identifiers to contained values class |
| CNamedAtomID_Map_NamedAtomID | |
| CNamedStubID | |
| CSequenceMapping | |
| CStubID | |
| CTorsionID | Torsion identifier class |
| CTorsionID_Range | Kinematics DOF identifier (with range) class |
| ►Nimport_pose | |
| ►Natom_tree_diffs | |
| CAtomTreeDiff | An object wrapper for reading atom_tree_diff files, complete with embedded reference structures |
| CScoreLessThanComparator | Provides a StrictWeakOrdering comparator for sorting elements of a ScoresMap by one particular score type |
| ►Nlibraries | |
| CBasePairStepLibrary | |
| CBasePairStepSequence | |
| CBasePairType | |
| CChunkSet | |
| CRNA_ChunkLibrary | |
| CRNA_JumpLibrary | |
| CRNA_LibraryManager | Holds all libraries relevant to FARFAR as CONST copies: |
| CRNA_PairingTemplate | |
| ►Noptions | |
| CRNA_BasicOptions | |
| CRNA_DeNovoProtocolOptions | |
| CRNA_FragmentMonteCarloOptions | |
| CRNA_MinimizerOptions | |
| ►Npose_stream | |
| CExtendedPoseInputStream | |
| CLazySilentFilePoseInputStream | |
| CMetaPoseInputStream | |
| CPDBPoseInputStream | |
| CPoseInputStream | |
| CSilentFilePoseInputStream | |
| CFullModelPoseBuilder | |
| CImportPoseOptions | 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! |
| CPDBSilentStruct | |
| CPDBSilentStructCreator | Creator for the PDBSilentStruct class |
| CPoseResource | |
| CPoseResourceLoader | |
| CPoseResourceLoaderCreator | |
| CRNA_BasePairHandler | |
| CRNA_DeNovoParameters | |
| CRNA_DeNovoSetup | |
| CRNA_HelixAssembler | The RNA de novo structure modeling protocol |
| CRNA_JumpMover | |
| ►Ninit | |
| Cpre_talaris_2013_behavior_settings | |
| ►Nio | |
| ►Nexternal | |
| CPsiPredInterface | |
| CPsiPredResult | |
| ►Nmmtf | |
| Cai_cmp | Simple comparator for AtomInformation when grouping by residue/grp |
| CExtraDataEnumManager | Enum string/enum functions for pose extra data we will be storing/retrieving. ALL enums must be defined in mmtf/ExtraDataEnum.hh |
| Csd_index | Storage for indicies to something in a mmtf struct this makes it easier to iterate the struct in relation to AtomInformation vectors |
| ►Nnmr | |
| CAtomSelection | |
| CParaIon | |
| CParamagneticDatabaseHandler | |
| CSpinlabelDatabaseEntry | |
| CSpinlabelDatabaseHandler | |
| ►Npdb | |
| CField | |
| CRecordCollection | |
| ►Npose_from_sfr | |
| CGeometricRenameIsomorphismCallback | |
| CGeometricRenameVerticiesEquivalent | Will consider two verticies equivalent if they have the same element |
| CGraphvizPropertyWriter | Callback class for writing graphviz info |
| CPoseFromSFRBuilder | The PoseFromSFRBuilder is responsible for taking a partially-processed representation of a structure file, a structure-file repersentation or StructFileRep, and it constructs a Pose from it. Its primary output is a Pose, but it also keeps track of the "missing atoms:" the set of atoms in the Pose whose coordinates were not given in the original file |
| ►Npose_to_sfr | |
| CPoseToStructFileRepConverter | A class to convert a pose to a StructFileRep |
| ►NPositionDdGInfo | |
| CPositionDdGInfo | Small helper class that stores the ddGs for mutations at a given position. camel case gets weird when trying to write words containing ddG.. |
| ►Nraw_data | |
| CDecoyFileData | |
| CDecoyStruct | |
| ►CDisulfideFile | Parses and stores a disulfide file |
| CResNum | Residue of either pdb or rosetta numbering |
| ►CRawFileData | 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 |
| Cconst_iterator | Const_iterator class for RawFileData container |
| Citerator | Iterator class for RawFileData container |
| CRawStruct | |
| CScoreFileData | |
| CScoreMap | |
| CScoreStructJSON | |
| CScoreStructText | |
| ►Nrna | |
| CRDAT | |
| CRNA_DataReader | |
| ►Nsequence_comparation | |
| CDesignContrast | 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 |
| ►Nserialization | |
| CBUFFER | |
| ►Nsilent | |
| CBinarySilentStruct | Why this inheritance pathway? this makes no sense! |
| CBinarySilentStructCreator | Creator for the BinarySilentStruct class |
| CEnergyNames | |
| CProteinSilentStruct_SinglePrecCreator | Creator for the ProteinSilentStruct_SinglePrec class |
| CProteinSilentStruct_Template | |
| CProteinSilentStructCreator | Creator for the ProteinSilentStruct class |
| CRigidBodySilentStruct | |
| CRigidBodySilentStructCreator | Creator for the RigidBodySilentStruct class |
| CRNA_SilentStruct | |
| CRNA_SilentStructCreator | Creator for the RNA_SilentStruct class |
| CScoreFileSilentStruct | |
| CScoreFileSilentStructCreator | Creator for the ScoreFileSilentStruct class |
| CScoreJumpFileSilentStruct | |
| CScoreJumpFileSilentStructCreator | Creator for the ScoreJumpFileSilentStruct class |
| CSharedSilentData | |
| CSilentEnergy | Helper class for silent-file classes to keep track of energy information |
| ►CSilentFileData | 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 |
| Cconst_iterator | Const_iterator class for SilentFileData container |
| Citerator | Iterator class for SilentFileData container |
| CSilentFileOptions | |
| CSilentStruct | |
| CSilentStructCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| CSilentStructFactory | |
| CSilentStructRegistrator | 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 |
| CSimpleSequenceData | |
| CAtomInformation | |
| CCisPeptideInformation | |
| CCrystInfo | |
| CHeaderInformation | Information stored in the Title Section records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z |
| CHELIXInformation | |
| CLinkInformation | |
| CModifiedResidueInformation | |
| CNomenclatureManager | |
| CRemarkInfo | |
| CRemarks | |
| CResidueInformation | |
| CSHEETInformation | |
| CSSBondInformation | |
| CStructFileReaderOptions | |
| CStructFileRep | |
| CStructFileRepOptions | |
| ►Nkinematics | |
| ►Njacobian | |
| CJacobianStructure | Upper-level wrapper of the Jacobian analysis of a protein's kinematics relations |
| ►CModuleType1 | Covers the Jacobian analysis at the lower-level for type-1 systems, which have internal DoFs that can be organized as three sets of two torsion angles with intersecting axes |
| Cjacobian_struct | Struct to pass around all variations of Jacobian matrices fw_dofs is the Jacobian matrix that maps differential torsion angles [rad/s] or [delta rad] on Cartesian reference frame fw_cons is the 6x6 Jacobian matrix that maps virtual (helper, constrained) torsion angles [rad/s] or [delta rad] on Cartesian reference frame fw_all is the 6x6 Jacobian matrix that maps all six torsion angles (real and virtual) [rad/s] or [delta rad] on Cartesian reference frame inv_dofs is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto torsion angles inv_cons is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto virtual torsion angles that represent the modules constraints inv_all is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto all torsion angles (real and virtual) |
| Cscrew_construct_struct | Struct with the different linear algebra objects that are needed to express the twists and wrenches to calculate the instantaneous Jacobian matrices of the module |
| CSeriesJacobians | Mid-level of the Jacobian analysis of a protein's kinematics relations |
| ►Ntree | |
| CAtom | Kinematics Atom interface class |
| CAtom_ | Kinematics Atom abstract base class |
| CBondedAtom | Atom which are bonded to its parent, derived from Atom_ |
| CJumpAtom | Atom who are connected to its parent via rigid-body transformation "Jump" |
| CAtomTree | Wrapper for a tree of kinematic Atoms |
| CAtomWithDOFChange | Simple class for use in output-sensitive refold subroutine |
| CEdge | Single edge of the fold_tree |
| CEXCN_InvalidFoldTree | |
| CFoldTree | The FoldTree is a residue-based tree-like representation of a molecule |
| CJump | Object which makes rigid-body transformation with translational and rotational perturbation |
| CMinimizerMapBase | |
| CMoveMap | A class specifying DOFs to be flexible or fixed |
| CNode | |
| CResidueCoordinateChangeList | 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 |
| CRT | Rotation + translation class |
| CShortestPathInFoldTree | |
| CStub | Stub class – an object of orthogonal coordinate frame |
| CTreeVizBuilder | |
| ►Noptimization | |
| ►Nsymmetry | |
| CMinDebug | |
| CSymAtomTreeMinimizer | High-level atom tree minimizer class |
| CSymAtomTreeMultifunc | Atom tree multifunction class |
| CSymMinimizerMap | Atom tree multifunction class |
| CArmijoLineMinimization | |
| CAtomTreeMinimizer | High-level atom tree minimizer class |
| CAtomTreeMultifunc | Atom tree multifunction class |
| CBrentLineMinimization | |
| CCartesianMinimizer | High-level atom tree minimizer class |
| CCartesianMinimizerMap | |
| CCartesianMultifunc | Atom tree multifunction class |
| CConvergenceTest | |
| CDerivCheckDataPoint | |
| CDescentDirectionAlgorithm | |
| CDFPMinConvergedAbsolute | |
| CDFPMinConvergedFractional | |
| CDOF_DataPoint | |
| CDOF_Node | |
| CEItem | Inner class for Genetic Algorithm, hold one population with some additional info |
| Cfunc_1d | |
| CGA_Minimizer | |
| CJJH_Minimizer | |
| Clbfgs_iteration_data | |
| CLineMinimizationAlgorithm | |
| CMinimizer | Simple low-level minimizer class |
| CMinimizerMap | |
| CMinimizerOptions | |
| CMultifunc | Multifunction interface class |
| CNelderMeadSimplex | |
| CNumDerivCheckData | |
| CNumericalDerivCheckResult | |
| CParticle | Simple data container for PSO algorithm |
| CParticleSwarmMinimizer | Particle Swarm Optimization engine |
| CSimpleDerivCheckResult | |
| CSingleResidueMultifunc | A streamlined AtomTreeMultifunc designed specifically for RTMIN |
| Csort_pred | |
| CStrongWolfeLineMinimization | |
| ►Npack | |
| ►Nannealer | |
| CAnnealerFactory | |
| CDebuggingAnnealer | |
| CFASTERAnnealer | |
| CFixbbCoupledRotamerSimAnnealer | |
| CFixbbLinkingRotamerSimAnnealer | |
| CFixbbPwatSimAnnealer | |
| CFixbbSimAnnealer | |
| CKey | |
| CKeyHasher | |
| CMultiCoolAnnealer | |
| CPointDwell | |
| CRotamerAssigningAnnealer | |
| CRotSub | |
| CSequenceSymmetricAnnealer | |
| CSimAnnealerBase | |
| CSmartFixbbSimAnnealer | |
| CValue | |
| ►Ndunbrack | |
| ►Ncenrot | |
| CCenRotDunEnergy | |
| CCenRotDunEnergyCreator | |
| CCenrotLibrary | Stores and handles loading of centroid rotamers for the canonical amino acids |
| CCentroidRotamerSampleData | Simple class storing all the data for one centroid-rotamer well |
| CSingleResidueCenrotLibrary | |
| CSingleResidueCenrotLibraryCreator | |
| CBBDepNRChiSample | P for precision |
| CBBDepScoreInterpData | |
| CBBDepSemiRotamericData | 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 |
| CBBIndNRChiSample | |
| CBBIndSemiRotamericData | 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 |
| CChiSet | |
| CDunbrackAAParameterSet | A small structure to hold overview parameters about the Dunbrack Libraries |
| CDunbrackConstraint | |
| CDunbrackConstraintCreator | Mover creator for the DunbrackConstraint constraint |
| CDunbrackEnergy | |
| CDunbrackEnergyCreator | |
| CDunbrackRotamer | Forward declaration; default precision is DunbrackReal |
| CDunbrackRotamerMeanSD | Forward declaration; default precision is DunbrackReal |
| CDunbrackRotamerSampleData | |
| CPackedDunbrackRotamer | Forward declaration; default precision is DunbrackReal; |
| CProbSortClass | |
| CRotamerBuildingData | 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 |
| CRotamerConstraint | This class favors a particular rotamer at a particular position by reducing its Dunbrack energy |
| CRotamericData | DOUG DOUG DOUG |
| CRotamericSingleResidueDunbrackLibrary | |
| CRotamericSingleResidueDunbrackLibraryParser | A helper class to assist in parsing rotamer libraries |
| CRotamerLibrary | A class to manage the Dunbrack Rotamer Libraries |
| CRotamerLibraryScratchSpace | |
| CSemiRotamericSingleResidueDunbrackLibrary | 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 |
| CSingleResidueDunbrackLibrary | |
| CSingleResidueDunbrackLibraryConcrete | |
| CSingleResidueDunbrackLibraryCreator | |
| ►Nguidance_scoreterms | |
| ►Napproximate_buried_unsat_penalty | |
| CApproximateBuriedUnsatPenalty | |
| CApproximateBuriedUnsatPenaltyCreator | |
| CHBondBonusOptions | |
| COversatToSidechain | |
| COversatToSidechainHasher | |
| CReweightData | |
| CScratchVectors | |
| CUnsatCorrectionOptions | |
| ►Nburied_unsat_penalty | |
| ►Ngraph | |
| CBuriedUnsatPenaltyEdge | Each BuriedUnsatPenaltyEdge represents a hydrogen bonding interaction between two residues, and stores information about (a) the number of hydrogen bonds, and (b) the atoms involved |
| CBuriedUnsatPenaltyEdgeData | |
| CBuriedUnsatPenaltyGraph | The BuriedUnsatPenaltyGraph consists of nodes representing resiudues (or rotamers in packing mode) and edges representing hydrogen-bonding interactions. Each node stores a list of hydrogen bond donor and acceptor atoms that we're seeking to satisfy; each edge stores the donors and acceptors that are connected by hydrogen bonds when two residues (or rotamers) interact |
| CBuriedUnsatPenaltyGraphContainer | A container for the BuriedUnsatPenaltyGraph, to allow it to be cached in a pose while skirting multiple inheritance issues |
| CBuriedUnsatPenaltyGraphHbond | A hydrogen bond between two atoms in two residues. Since this is tied to a BuriedUnsatPenaltyEdge (which in turn is associated with two residues), it stores only donor group index and acceptor group index. The group indices match the indexing in the corresponding node |
| CBuriedUnsatPenaltyGraphHbondDonorAcceptorGroup | A class for a hydrogen bond donor group or acceptor group |
| CBuriedUnsatPenaltyGraphOptions | Options container for the BuriedUnsatPenaltyGraph. Initialized by the BuriedUnsatPenalty energy method |
| CBuriedUnsatPenaltyNode | Each BuriedUnsatPenaltyNode represents a rotamer from the RotamerSets object, or a residue (if we're doing a simple scoring pass) |
| CBuriedUnsatPenaltyNodeData | Data stored inside a BuriedUnsatPenaltyNode |
| CBuriedUnsatPenalty | BuriedUnsatPenalty, an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors or acceptors |
| CBuriedUnsatPenaltyCreator | |
| ►Nhbnet_energy | |
| CHBNetEnergy | HBNetEnergy, an EnergyMethod that gives a bonus for hydrogen bond networks, which ramps nonlinearly with the size of the networks. This class is derived from base class WholeStructureEnergy, which is meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of scorefunction evaluation |
| CHBNetEnergyCreator | |
| ►Nvoids_penalty_energy | |
| CVoidsPenaltyEnergy | VoidsPenaltyEnergy ("voids_penalty" score term), an EnergyMethod intended for packing, which penalizes solutions in which the total volume to fill differs greatly from the total volume of the current set of rotamers |
| CVoidsPenaltyEnergyCreator | |
| CVoidsPenaltyVoxelGrid | A 3D boolean array used for identifying core voxels in the VoidsPenaltyEnergy |
| ►Nhbonds | |
| CBareMinimumPDEdge | |
| CHBondGraphInitializerIG | |
| ►Ninteraction_graph | |
| CAdditionalBackgroundNodesInteractionGraph | Function declarations for the AdditionalBackgroundNodesInteractionGraph |
| CAminoAcidNeighborSparseMatrix | |
| CAnnealableGraphBase | |
| CBackgroundNode | A node which is not changing type or rotamer throughout a simulation |
| CBackgroundToFirstClassEdge | An edge between a background node and a first class node |
| CDensePDEdge | |
| CDensePDInteractionGraph | |
| CDensePDNode | |
| CDotSphere | Represents the sphere of dots on the vdW surface of an atom, for use in the LeGrand and Merz method of calculating SASA |
| CDoubleDensePDEdge | |
| CDoubleDensePDInteractionGraph | |
| CDoubleDensePDNode | |
| CDoubleLazyEdge | |
| CDoubleLazyInteractionGraph | 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 |
| CDoubleLazyNode | |
| CEdgeBase | |
| Cexposed_hydrophobic_data | |
| CFASTEREdge | |
| CFASTERInteractionGraph | |
| CFASTERNode | |
| CFirstClassEdge | |
| CFirstClassNode | |
| CFixedBBEdge | |
| CFixedBBInteractionGraph | |
| CFixedBBNode | |
| Chistory_queue_struct | For storing three peices of associated data describing the recent history structure on a LinearMemNode |
| CHPatchBackgroundEdge | Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) |
| CHPatchBackgroundNode | 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 |
| CHPatchEdge | 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 |
| CHPatchEnergy | 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 |
| CHPatchEnergyCreator | |
| CHPatchInteractionGraph | Defines the interaction graph that will keep track of changes to the hpatch score |
| CHPatchNode | Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph |
| CInteractionGraphBase | |
| CInteractionGraphFactory | |
| CInvRotamerDots | Used to determine whether the overlap between two atoms is buried or exposed |
| CLazyEdge | |
| CLazyInteractionGraph | |
| CLazyNode | |
| CLinearMemEdge | |
| CLinearMemNode | |
| CLinearMemoryInteractionGraph | |
| CMultiplexedAnnealableGraph | |
| CNodeBase | |
| CNPDHBond | |
| CNPDHBondBackgroundEdge | Defines an edge between a FirstClass (NPDHBondNode) and a background node (NPDHBondBackgroundNode) |
| CNPDHBondBackgroundNode | 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 |
| CNPDHBondEdge | Defines a NPDHBond Edge which connects two first-class NPDHBond Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast |
| CNPDHBondInteractionGraph | Defines the interaction graph that will keep track of changes to the hpatch score |
| CNPDHBondNode | Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph |
| CNPDHBSimpleEdge | |
| CNPDHBSimpleInteractionGraph | 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 |
| CNPDHBSimpleNode | |
| COnTheFlyEdge | |
| COnTheFlyInteractionGraph | |
| COnTheFlyNode | |
| CPDEdge | |
| CPDInteractionGraph | |
| CPDNode | |
| CPrecomputedPairEnergiesEdge | |
| CPrecomputedPairEnergiesInteractionGraph | |
| CPrecomputedPairEnergiesNode | |
| CResidueArrayAnnealingEvaluator | |
| CRotamerDots | Handles sphere-sphere overlap calculations for the HPatchInteractionGraph |
| CRotamerDotsCache | A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes |
| CRotamerDotsRadiusData | A singleton class which reads in database SASA radii files and provides accessors for those values to the RotamerDots class |
| CSimpleEdge | |
| CSimpleInteractionGraph | 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 |
| CSimpleNode | |
| CSparseMatrixIndex | |
| CSurfaceBackgroundEdge | Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) |
| CSurfaceBackgroundNode | 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 |
| CSurfaceEdge | Defines a Surface edge which will be used in determining surface energy |
| CSurfaceEnergy | 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 |
| CSurfaceEnergyCreator | |
| CSurfaceInteractionGraph | Defines the interaction graph that will keep track of changes to the surface score |
| CSurfaceNode | Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph |
| CSurfacePotential | With the traditional scoring hierarchy, classes like this one are created and accessed via the ScoringManager, which is itself a Singleton class. These "potential" classes are only created and initialized when the use of the EnergyMethod these classes correspond is encountered. No point in reading database files for a term if that term is not being used in some score function. However, the surface energy is used when users specify they want to use it on the command line - NOT via a score function. The score/energy is done within an interaction graph. One might ask why I just don't put the logic for reading in the database file to the interaction graph init methods. However, there will be cases where I will want to just score a protein (and not do any design) where I will want the database file to be read in. Scoring doesn't use interaction graphs, so if the code for that was located there, these values would not be read in. Instead, I've decided to implement this as its own separate class. It uses the Singleton design pattern so the database will only get read in once during a run |
| CSymmLinearMemEdge | |
| CSymmLinearMemNode | |
| CSymmLinearMemoryInteractionGraph | |
| CSymmMinimalistEdge | |
| CSymmMinimalistInteractionGraph | |
| CSymmMinimalistNode | |
| CSymmOnTheFlyEdge | |
| CSymmOnTheFlyInteractionGraph | |
| CSymmOnTheFlyNode | |
| ►Npalette | |
| CBaseTypeList | A small utility class which allows you to do a map-like addition of name/ResidueType pairs, but keeps things in the added order |
| CCustomBaseTypePackerPalette | CustomBaseTypePackerPalette: a PackerPalette that allows a user to define additional ResidueTypes with which to design (but not additional VariantTypes, at this time) |
| CCustomBaseTypePackerPaletteCreator | The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class |
| CDefaultPackerPalette | Gives instructions to the packer about the set of ResidueTypes and VariantTypes to use by default, in the absence of any TaskOperations that prune the list. Specifically, the DefaultPackerPalette says, "By default, use the twenty canonical amino acids and whatever is present at a given position -- and
nothing else." |
| CDefaultPackerPaletteCreator | The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class |
| CNCAADefaultPackerPalette | Gives instructions to the packer about the set of ResidueTypes and VariantTypes to use by default, in the absence of any TaskOperations that prune the list. Specifically, the NCAADefaultPackerPalette says, "By default, use the twenty canonical amino acids and whatever is present at a given position -- and
nothing else." |
| CNCAADefaultPackerPaletteCreator | The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class |
| CNoDesignPackerPalette | Gives instructions to the packer about the set of ResidueTypes and VariantTypes to use by default, in the absence of any TaskOperations that prune the list. Specifically, the NoDesignPackerPalette says, "By default, use the twenty canonical amino acids and whatever is present at a given position -- and
nothing else." |
| CNoDesignPackerPaletteCreator | The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class |
| CPackerPalette | Gives instructions to the packer about the set of ResidueTypes and VariantTypes to use by default, in the absence of any TaskOperations that prune the list |
| CPackerPaletteCreator | The PackerPaletteCreator class's responsibilities are to create on demand a new instance of a PackerPalette class |
| CPackerPaletteFactory | |
| CPackerPaletteRegistrator | This templated class will register an instance of an PackerPalettteCreator (class T) with the PackerPaletteFactory. It will ensure that no PackerPaletteCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| ►Nrotamer_set | |
| ►Nsymmetry | |
| CSymmetricRotamerSet_ | 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_ |
| CSymmetricRotamerSets | |
| CAddResiduesRotamerSetOperation | Adds in rotamers from a list of Residues, |
| CBumpSelector | |
| CContinuousRotamerSet | |
| CContinuousRotamerSets | |
| CDeleteAllRotamerSetOperation | Adds in rotamers from a list of Residues, |
| CFixbbRotamerSets | |
| CRotamerCouplings | |
| CRotamerLinks | |
| CRotamerOperation | RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation |
| CRotamerSet | |
| CRotamerSet_ | 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 |
| CRotamerSetFactory | |
| CRotamerSetOperation | |
| CRotamerSets | |
| CRotamerSetsFactory | |
| CRotamerSetsOperation | RotamerSetsOperations are able to modify the RotamerSets object such that changes can be correlated accros multiple rotamer sets |
| CRotamerSubset | 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) |
| CRotamerSubsets | |
| CUnboundRotamersOperation | Adds in rotamers from the "unbound" or native structure(s), pulled from one or more PDBs supplied on the command line |
| CWaterAnchorInfo | |
| CWaterPackingInfo | |
| ►Nrotamers | |
| CSingleBasicRotamerLibrary | A simple Rotamer library, which serves as a default for ResidueTypes which don't have some other more specific rotamer library |
| CSingleBasicRotamerLibraryCreator | |
| CSingleLigandRotamerLibrary | A fixed library of conformations for some residue type (doesn't have to be a ligand) |
| CSingleLigandRotamerLibraryCreator | |
| CSingleNCAARotamerLibraryCreator | |
| CSingleResidueRotamerLibrary | SingleResidueRotamerLibrary pure virtual base class |
| CSingleResidueRotamerLibraryCreator | |
| CSingleResidueRotamerLibraryFactory | |
| CSingleResidueRotamerLibraryRegistrator | This templated class will register an instance of an SingleResidueRotamerLibraryCreator (class T) with the SingleResidueRotamerLibraryFactory. It will ensure that no SingleResidueRotamerLibrary creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CStoredRotamerLibraryCreator | |
| ►Nscmin | |
| CAtomTreeCollection | A collection of ResidueAtomTreeCollection objects for an entire design task |
| CAtomTreeSCMinMinimizerMap | |
| CCartSCMinMinimizerMap | |
| CCartSCMinMultifunc | |
| CResidueAtomTreeCollection | 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 |
| CResidueAtomTreeCollectionMomento | Class to save the state for a ResidueAtomTreeCollection |
| CSCMinMinimizerMap | |
| CSCMinMultifunc | |
| CSidechainStateAssignment | A simple class for tracking a network state and its energy where each sidechain's state is described by a series of chi angles |
| ►Ntask | |
| ►Noperation | |
| CAddBehaviorRLT | |
| CAddBehaviorRLTCreator | |
| CAllResFilter | |
| CAllResFilterCreator | |
| CAnyResFilter | |
| CAnyResFilterCreator | |
| CAppendResidueRotamerSet | Apply rotamerSetOperation to only the rotamerSet for the given residue |
| CAppendResidueRotamerSetCreator | |
| CAppendRotamer | When a PackerTask is created by the Factory, the RotamerOperation will be given to it |
| CAppendRotamerCreator | |
| CAppendRotamerSet | When a PackerTask is created by the Factory, the RotamerSetOperation will be given to it |
| CAppendRotamerSetCreator | |
| CChainIs | |
| CChainIsCreator | |
| CChainIsnt | |
| CChainIsntCreator | |
| CClashBasedRepackShell | Create a shell of residues that can repack around a smaller group of residues being repacked or designed |
| CClashBasedRepackShellCreator | |
| CDesignRestrictions | Combine a set of ResidueSelectors and ResidueLevelTaskOperations concisely, using boolean logic to join selectors concisely |
| CDesignRestrictionsCreator | |
| CDisallowIfNonnative | 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 |
| CDisallowIfNonnativeCreator | |
| CDisallowIfNonnativeRLT | |
| CDisallowIfNonnativeRLTCreator | |
| CEnableMultiCoolAnnealer | Task Operation for turning on the multi-cool annealer |
| CEnableMultiCoolAnnealerCreator | |
| CEnableSmartAnnealer | Task Operation for turning on the multi-cool annealer |
| CEnableSmartAnnealerCreator | |
| CExtraChiCutoff | ExtraChiCutoff (correponding to flag "-extrachi_cutoff <float>" ) |
| CExtraChiCutoffCreator | |
| CExtraChiCutoffRLT | |
| CExtraChiCutoffRLTCreator | |
| CExtraRotamers | ExtraRotamer for a residue. You know, -ex1, -ex2, all that |
| CExtraRotamerSamplingData | |
| CExtraRotamersCreator | |
| CExtraRotamersGeneric | |
| CExtraRotamersGenericCreator | |
| CExtraRotamersGenericRLT | |
| CExtraRotamersGenericRLTCreator | |
| CFillAUTOTaskOperation | Fills the AUTO behavior for all residues in Task. Useful if a protocol expects AUTO-style resfile, but no resfile present |
| CFillAUTOTaskOperationCreator | |
| CIncludeCurrent | |
| CIncludeCurrentCreator | |
| CIncludeCurrentRLT | |
| CIncludeCurrentRLTCreator | |
| CInitializeExtraRotsFromCommandline | |
| CInitializeExtraRotsFromCommandlineCreator | |
| CInitializeFromCommandline | |
| CInitializeFromCommandlineCreator | |
| CInitializeFromOptionCollection | Retrieves an OptionCollection from the DataMap |
| CInitializeFromOptionCollectionCreator | |
| CKeepSequenceSymmetry | Task Operation for turning on the multi-cool annealer |
| CKeepSequenceSymmetryCreator | |
| CNoRepackDisulfides | Prevent disulfides from being repacked; assume disulfides info in Pose is up-to-date |
| CNoRepackDisulfidesCreator | |
| CNoResFilter | |
| CNoResFilterCreator | |
| COperateOnCertainResidues | |
| COperateOnCertainResiduesCreator | |
| COperateOnResidueSubset | Class, much like the OperateOnCertainResidues task operation, to apply a particular residue-level task operation on the residues identified by a ResidueSelector (Or a pre-selected subset) |
| COperateOnResidueSubsetCreator | |
| COptCysHG | Run optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides() |
| COptCysHGCreator | |
| COptH | Run optH; disallowed positions may be set to prevent optimization for those residues |
| COptHCreator | |
| CPreserveCBeta | |
| CPreserveCBetaCreator | |
| CPreserveCBetaRLT | |
| CPreserveCBetaRLTCreator | |
| CPreventRepacking | 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 |
| CPreventRepackingCreator | |
| CPreventRepackingRLT | |
| CPreventRepackingRLTCreator | |
| CProhibitResidueProperties | Restrict the palette of ResidueTypes to those with the given properties |
| CProhibitResiduePropertiesCreator | |
| CProhibitSpecifiedBaseResidueTypes | Prohibit the base ResidueTypes provided by name from the palette of ResidueTypes |
| CProhibitSpecifiedBaseResidueTypesCreator | |
| CReadResfile | |
| CReadResfileAndObeyLengthEvents | 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 |
| CReadResfileAndObeyLengthEventsCreator | |
| CReadResfileCreator | |
| CReplicateTask | |
| CResFilter | |
| CResFilterComposition | |
| CResFilterCreator | 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 |
| CResFilterFactory | |
| CResFilterRegistrator | 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 |
| CResidueHasProperty | |
| CResidueHasPropertyCreator | |
| CResidueIndexIs | |
| CResidueIndexIsCreator | |
| CResidueIndexIsnt | |
| CResidueIndexIsntCreator | |
| CResidueLacksProperty | |
| CResidueLacksPropertyCreator | |
| CResidueName3Is | |
| CResidueName3IsCreator | |
| CResidueName3Isnt | |
| CResidueName3IsntCreator | |
| ►CResiduePDBIndexIs | |
| CChainPos | |
| CResiduePDBIndexIsCreator | |
| CResiduePDBIndexIsnt | |
| CResiduePDBIndexIsntCreator | |
| CResiduePDBInfoHasLabel | |
| CResiduePDBInfoHasLabelCreator | |
| CResiduePDBInfoLacksLabel | |
| CResiduePDBInfoLacksLabelCreator | |
| CResidueTypeFilter | |
| CResidueTypeFilterCreator | |
| CResLvlTaskOperation | |
| CResLvlTaskOperationCreator | 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 |
| CResLvlTaskOperationFactory | |
| CResLvlTaskOperationRegistrator | 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 |
| CRestrictAbsentCanonicalAAS | RestrictAbsentCanonicalAAS |
| CRestrictAbsentCanonicalAASCreator | |
| CRestrictAbsentCanonicalAASExceptNativeRLT | |
| CRestrictAbsentCanonicalAASExceptNativeRLTCreator | |
| CRestrictAbsentCanonicalAASRLT | |
| CRestrictAbsentCanonicalAASRLTCreator | |
| CRestrictInteractionGraphThreadsOperation | A task operation that restricts the number of threads allowed for interaction graph computation |
| CRestrictInteractionGraphThreadsOperationCreator | |
| CRestrictResidueToRepacking | RestrictResidueToRepacking |
| CRestrictResidueToRepackingCreator | |
| CRestrictToRepacking | RestrictToRepacking |
| CRestrictToRepackingCreator | |
| CRestrictToRepackingRLT | |
| CRestrictToRepackingRLTCreator | |
| CRestrictToResidueProperties | Restrict the palette of ResidueTypes to those with the given properties |
| CRestrictToResiduePropertiesCreator | |
| CRestrictToSpecifiedBaseResidueTypes | Restrict the palette of ResidueTypes to the base ResidueTypes provided by name |
| CRestrictToSpecifiedBaseResidueTypesCreator | |
| CRestrictYSDesign | RestrictYSDesign restricts positions to a binary Tyr/Ser alphabet |
| CRestrictYSDesignCreator | |
| CRotamerExplosion | Rotamer explosion for a residue |
| CRotamerExplosionCreator | |
| CSetRotamerCouplings | |
| CSetRotamerCouplingsCreator | |
| CSetRotamerLinks | |
| CSetRotamerLinksCreator | |
| CTaskOperation | |
| CTaskOperationCreator | 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 |
| CTaskOperationFactory | |
| CTaskOperationRegistrator | 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 |
| CUseMultiCoolAnnealer | |
| CUseMultiCoolAnnealerCreator | |
| ►Nresidue_selector | |
| CClashBasedShellSelector | Define a shell based on potential sidechain clashes with a set of residues being repacked or designed |
| CClashBasedShellSelectorCreator | |
| ►Nrna | |
| CRNA_ResidueLevelTask | |
| CALLAA | ALLAA is deprecated; allows repacking and designing to any canonical residue (default state of PackerTask) |
| CALLAAwc | Allows repacking and designing to any canonical residue (default state of PackerTask) |
| CALLAAxc | ALLAAxc allows repacking and designing to any canonical noncysteine residue |
| CAPOLA | APOLA is a deprecated version of APOLAR allows nonpolar residues and packing |
| CAPOLAR | APOLAR allows nonpolar residues and packing |
| CAROMATIC | AROMATIC allows designing only aromatic residues. JAB |
| CAUTO | AUTO suggests that a packer can/should reconsider the design setting at a/each residue |
| CCHARGED | CHARGED allows charged residues and packing JAB |
| CEX | EX handles the various extrachi options |
| CEX_CUTOFF | EX_CUTOFF allows setting of the extrachi_cutoff (for determining burial for extra rotamers) |
| CFIX_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) |
| CIGEdgeReweightContainer | Class that interfaces to containers holding IGedge weights between individual residues of the task |
| CIGEdgeReweighter | Helper class for IGEdgeReweightContainer |
| CNATAA | NATAA allows repacking but no sequence changes (all rotamers are of the original residue) |
| CNATRO | NATRO disables packing and designing at a position, the residue will be totally unchanged |
| CNO_ADDUCTS | NO_ADDUCTS will disable adducts, assuming they exist |
| CNOTAA | NOTAA disallows residues specified in a following string, and allows packing |
| CPackerTask | Task class that gives instructions to the packer |
| CPackerTask_ | PackerTask controls what rotameric (including sequence) changes the packer is allowed to make |
| CPIKAA | PIKAA allows residues specifed in a following string |
| CPIKNA | PIKNA allows nucleic acid residues specifed in a following string |
| CPOLAR | POLAR allows polar residues and packing |
| CPROPERTY | Allows designing on ANY residue type Property. (Only currently works with Cannonical AAs) JAB |
| CResfileCommand | Abstract/interface class for Resfile reader command objects |
| CResfileContents | |
| CResfileReaderException | |
| CResidueLevelTask | |
| CResidueLevelTask_ | Residue-level task class |
| CSCAN | 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 |
| CTARGET | TARGET flags the position as "targeted", and can optionally specify a "targeted" type |
| CTaskFactory | Factory class for the creation and initialization of PackerTask objects |
| CUSE_INPUT_SC | USE_INPUT_SC turns on inclusion of the current rotamer for the packer |
| CRTMin | |
| ►Npack_basic | |
| CRotamerSetsBase | |
| ►Npose | |
| ►Ncopydofs | |
| CCopyDofs | |
| CCopyDofsInfo | |
| ►Ndatacache | |
| CCacheableDataType | |
| CCacheableObserver | Base class for Pose/Conformation observers that are stored in a Pose's DataCache |
| CCacheablePoseRawPtr | Holds a smart pointer (no longer a raw pointer) to a Pose so that it can be tucked inside another Pose |
| CLengthEventCollector | Cacheable observer that keeps track of what length events occured |
| CObserverCache | A DataCache storing Pose/Conformation observers derived from core::pose::datacache::CacheableObserver |
| CPositionConservedResiduesStore | |
| CSpecialSegmentsObserver | 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 |
| ►Nfull_model_info | |
| CFullModelInfo | Keep track of all information related to how a subpose 'fits in' to global modeling scheme |
| CFullModelParameters | |
| CSubMotifInfo | Keep track of information about a submotif added to a pose |
| ►Nmetrics | |
| ►Nsimple_calculators | |
| CInterfaceDefinitionCalculator | |
| CInterfaceDeltaEnergeticsCalculator | |
| CInterfaceNeighborDefinitionCalculator | |
| CInterfaceSasaDefinitionCalculator | |
| CSasaCalculator2 | |
| CSasaCalculatorLegacy | |
| CCalculatorFactory | |
| CEnergyDependentCalculator | |
| CPoseMetricCalculator | |
| CPoseMetricContainer | Container for managing PoseMetricCalculators |
| CStructureDependentCalculator | |
| ►Nreference_pose | |
| CReferencePose | ReferencePose class, used to store sets of ReferencePose data for tracking how a pose changes over the course of a protocol |
| CReferencePoseSet | ReferencePoseSet class, used to store sets of ReferencePose data for tracking how a pose changes over the course of a protocol |
| ►Nrna | |
| ►Nsecstruct_legacy | |
| CRNA_SecStructLegacyInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| CAtom_Bin | |
| CBasePair | |
| CBasePairStep | |
| CBaseStack | |
| Cprincipal_angle_degrees | |
| CRNA_DataInfo | Keep track of RNA chemical mapping data inside the pose |
| CRNA_Datum | |
| CRNA_FilteredBaseBaseInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| CRNA_IdealCoord | |
| CRNA_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 (!) / |
| CRNA_Reactivity | |
| CRNA_SecStruct | |
| CRNA_SuiteAssignment | |
| CRNA_SuiteInfo | |
| CRNA_SuiteName | |
| CVDW_Grid | |
| CVDW_RepScreenInfo | |
| ►Nsignals | |
| CConformationEvent | Signals a conformation change in a Pose |
| CDestructionEvent | Special signal that the Pose is getting destroyed |
| CEnergyEvent | Signals an energy change in a Pose |
| CGeneralEvent | Signals a general change in a Pose |
| ►Ntoolbox | |
| CAtomID_Mapper | |
| CAtomLevelDomainMap | |
| CMiniPose | Lightweight version of the pose with stuff I need |
| ►CPDBInfo | Maintains pdb residue & atom information inside a Pose |
| CAtomRecord | Internal struct for storing PDB atom related information |
| CResidueRecord | Internal struct for storing PDB residue related information |
| ►CPDBPoseMap | 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 |
| Cno_segID_comp | |
| CResidueKey | Sortable residue key internal to PDBPoseMap |
| CPose | A molecular system including residues, kinematics, and energies |
| CResidueIndexDescription | 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 |
| CResidueIndexDescriptionChainEnd | Class which represents the last residue in the Pose |
| CResidueIndexDescriptionLastResidue | Class which represents the last residue in the Pose |
| CResidueIndexDescriptionPDB | Class which represents a residue index as a PDB information (chain, resindex, insertion code) |
| CResidueIndexDescriptionPoseNum | Class which represents a residue index as a literal, Rosetta/Pose numbered integer |
| CResidueIndexDescriptionRefPose | Class which represents a residue index as a reference-pose enabled information |
| CRID_FileSource | Representation of a file input support A class to hold information about where a ResidueIndexDescriptor comes from, to allow for better error messages |
| CRID_Source | A class to hold information about where a ResidueIndexDescriptor comes from, to allow for better error messages |
| CUnrecognizedAtomRecord | Info about an atom in a unrecognized res (not in pose, but we want to remember it) |
| CxyzStripeHashPose | |
| ►Nscoring | |
| ►Naa_composition_energy | |
| CAACompositionConstraint | |
| CAACompositionEnergy | AACompositionEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation |
| CAACompositionEnergyCreator | |
| CAACompositionEnergySetup | AACompositionEnergySetup, a helper class for the AACompositionEnergy energy method that stores all of its setup data |
| CAACompositionPropertiesSet | AACompositionPropertiesSet, a helper class that stores: |
| CSequenceConstraint | |
| ►Naa_repeat_energy | |
| CAARepeatEnergy | AARepeatEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation |
| CAARepeatEnergyCreator | |
| ►Nannealing | |
| CResidueArrayAnnealableEnergy | |
| ►Natomic_depth | |
| CAtomicDepth | |
| Cpoint3d | |
| Cvolumepixel | |
| Cvoxel | |
| Cvoxel2 | |
| ►Nbin_transitions | |
| CBinTransitionCalculator | |
| CBinTransitionData | |
| ►Ncarbohydrates | |
| CCHIDihedralSamplingData | Struct for CHI-based dihedral sampling |
| CCHIEnergyFunction | |
| COmegaPreferenceSamplingData | Struct for Omega-Preference dihedral sampling |
| COmegaPreferencesFunction | |
| ►Ncarbon_hbonds | |
| CCarbonHBondEnergy | |
| CCarbonHBondEnergyCreator | |
| CCarbonHBondPotential | |
| ►Nconstraints | |
| CAmbiguousConstraint | Nested constraint where only the one with lowest energy is considered |
| CAmbiguousConstraintCreator | Constraint creator for the AmbiguousConstraint constraint |
| CAmbiguousNMRConstraint | |
| CAmbiguousNMRConstraintCreator | Constraint creator for the AmbiguousNMRConstraint constraint |
| CAmbiguousNMRDistanceConstraint | |
| CAmbiguousNMRDistanceConstraintCreator | Constraint creator for the AmbiguousNMRDistanceConstraint constraint |
| CAngleConstraint | An Angular Constraint |
| CAngleConstraintCreator | Constraint creator for the AngleConstraint constraint |
| CAtomPairConstraint | |
| CAtomPairConstraintCreator | Constraint creator for the AtomPairConstraint constraint |
| CBackboneStubConstraint | This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location |
| CBackboneStubLinearConstraint | This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location |
| CBasePairConstraint | |
| CBasePairConstraintCreator | Constraint creator for the BasePairConstraint constraint |
| CBigBinConstraint | Constraint on dihedral angle formed by 4 points |
| CBigBinConstraintCreator | Constraint creator for the BigBinConstraint constraint |
| CBoundFunc | |
| CConstantConstraint | A Constant Constraint |
| CConstraint | Actually a restraint, like a virtual rubber band between a pair of atoms |
| CConstraintCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| CConstraintEdge | |
| CConstraintFactory | |
| CConstraintGraph | |
| CConstraintIO | |
| CConstraintNode | |
| CConstraintRegistrator | 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 |
| CConstraints | |
| CConstraintsEnergy | |
| CConstraintsEnergyCreator | |
| CConstraintSet | |
| CCoordinateConstraint | |
| CCoordinateConstraintCreator | Constraint creator for the CoordinateConstraint constraint |
| CCstEnergyContainer | |
| CCstMinimizationData | |
| CCstResNeighbConstIterator | |
| CCstResNeighbIterator | |
| CDihedralConstraint | Constraint on dihedral angle formed by 4 points |
| CDihedralConstraintCreator | Constraint creator for the DihedralConstraint constraint |
| CDihedralPairConstraint | Constraint on dihedral angle formed by 4 points |
| CDihedralPairConstraintCreator | Constraint creator for DihedralPairConstraint |
| CDistancePairConstraint | Constraint on CA distance |
| CDOF_Constraint | This isn't quite a standard constraint since it acts on DOF's directly rather than on XYZ coordinates |
| CFabConstraint | |
| CFabConstraintCreator | Constraint creator for the FabConstraint constraint |
| CKofNConstraint | |
| CKofNConstraintCreator | Constraint creator for the KofNConstraint constraint |
| CLocalCoordinateConstraint | |
| CLocalCoordinateConstraintCreator | Constraint creator for the LocalCoordinateConstraint constraint |
| CMembraneSpanConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| CMembraneSpanTermZConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| ►CMultiConstraint | |
| Cdont_copy_constraints | |
| CMultiConstraintCreator | Constraint creator for the MultiConstraint constraint |
| CNamedAngleConstraint | |
| CNamedAngleConstraintCreator | Constraint creator for the NamedAngleConstraint |
| CNamedAtomPairConstraint | |
| CNamedAtomPairConstraintCreator | Constraint creator for the NamedAtomPairConstraint constraint |
| CNamedDihedralConstraint | |
| CNonResidueTypeConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| CObsolet_NamedAtomPairConstraint | |
| COffsetPeriodicBoundFunc | Variant of the bound func that is periodic |
| CPeriodicBoundFunc | Variant of the bound func that is periodic |
| CResidueConstraints | |
| CResidueTypeConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| CResidueTypeLinkingConstraint | This class favors a particular residue identity at a particular position by reducing its res_type energy |
| CRTConstraint | |
| CSequenceProfileConstraint | |
| CSequenceProfileConstraintCreator | Constraint creator for the SequenceProfileConstraint constraint |
| CSiteConstraint | |
| CSiteConstraintCreator | Constraint creator for the SiteConstraint constraint |
| CSiteConstraintResidues | |
| CSiteConstraintResiduesCreator | Constraint creator for the SiteConstraintResidues constraint |
| ►Ncryst | |
| CPhenixInterface | |
| CXtalMLEnergy | |
| CXtalMLEnergyCreator | |
| ►Ncustom_pair_distance | |
| CAtomPairFuncList | |
| Catoms_and_func_struct | |
| CDistanceFunc | |
| CFullatomCustomPairDistanceEnergy | |
| CFullatomCustomPairDistanceEnergyCreator | |
| CPairFuncMap | |
| Cresatom_and_func_struct | |
| CRespairInteractions | |
| ►Ndisulfides | |
| CCaCbCb_Angle_Func | |
| CCaCbCbCa_Dihedral_Func | |
| CCB_Angle_Func | |
| CCb_Distance_Func | Score based on the distance between Cb |
| CCBSG_Dihedral_Func | |
| CCen_Distance_Func | |
| CCentroidDisulfideEnergy | |
| CCentroidDisulfideEnergyComponents | Storage for Disulfide Energy Terms |
| CCentroidDisulfideEnergyContainer | |
| CCentroidDisulfideEnergyCreator | |
| CCentroidDisulfideNeighborConstIterator | Just a const version of CentroidDisulfideNeighborIterator |
| CCentroidDisulfideNeighborIterator | An iterator over the disulfide bonds a residue forms |
| CCentroidDisulfidePotential | |
| CDisulfideAtomIndices | 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 |
| CDisulfideMatchingDatabase | |
| CDisulfideMatchingEnergy | |
| CDisulfideMatchingEnergyComponents | Storage for Disulfide Energy Terms |
| CDisulfideMatchingEnergyContainer | |
| CDisulfideMatchingEnergyCreator | |
| CDisulfideMatchingNeighborConstIterator | Just a const version of DisulfideMatchingNeighborIterator |
| CDisulfideMatchingNeighborIterator | An iterator over the disulfide bonds a residue forms |
| CDisulfideMatchingPotential | |
| CDisulfMinData | |
| CDisulfResNeighbConstIterator | |
| CDisulfResNeighbIterator | |
| CFullatomDisulfideEnergy | |
| CFullatomDisulfideEnergyComponents | |
| CFullatomDisulfideEnergyContainer | |
| CFullatomDisulfideEnergyCreator | |
| CFullatomDisulfideParams13 | |
| CFullatomDisulfidePotential | |
| CNCaCaC_Dihedral_Func | |
| CRT_helper | |
| CSG_Dist_Func | |
| CSGSG_Dihedral_Func | |
| ►Ndna | |
| CBasePartner | Silly vector1 wrapper class so we can derive from PoseCachedData |
| CDirectReadoutPotential | 1st pass implementation of Kono + Sarai's protein-DNA interaction potential |
| CDNA_BasePotential | |
| CDNA_DihedralPotential | |
| CDNA_EnvPairPotential | |
| CDNABFormPotential | |
| CDNAChiEnergy | |
| CDNAChiEnergyCreator | |
| CDNATorsionEnergy | |
| CDNATorsionEnergyCreator | |
| CDNATorsionPotential | |
| CTorsionFourierComponent | |
| ►Ndssp | |
| CDssp | |
| CPairing | |
| CStrandPairing | |
| CStrandPairingSet | |
| ►Nelec | |
| ►Nelectrie | |
| CElecAtom | |
| CElecTrieEvaluator | |
| CCountPairRepMap | A class to encapsulate the raw-pointer-based data caching |
| CCountPairRepresentative | |
| CElecGroup | |
| CFA_ElecEnergy | |
| CFA_ElecEnergyAroAll | |
| CFA_ElecEnergyAroAllCreator | |
| CFA_ElecEnergyAroAro | |
| CFA_ElecEnergyAroAroCreator | |
| CFA_ElecEnergyCreator | |
| CFA_GrpElecEnergy | |
| CFA_GrpElecEnergyCreator | |
| CFAElecContextData | |
| CGroupElec | |
| CRNA_FA_ElecEnergy | |
| CRNA_FA_ElecEnergyCreator | |
| Cweight_triple | |
| ►Nelectron_density | |
| CElecDensAllAtomCenEnergy | |
| CElecDensAllAtomCenEnergyCreator | |
| CElecDensCenEnergy | |
| CElecDensCenEnergyCreator | |
| CElecDensEnergy | |
| CElecDensEnergyCreator | |
| CElectronDensity | |
| CFastDensEnergy | |
| CFastDensEnergyCreator | |
| CKromerMann | |
| COneGaussianScattering | |
| CposeCoord | |
| ►Nelectron_density_atomwise | |
| CElecDensAtomwiseEnergy | |
| CElecDensAtomwiseEnergyCreator | |
| CElectronDensityAtomwise | |
| CPoseSequence | |
| ►Nepr_deer | |
| CDEERData | Base class |
| CDEERDataCache | |
| CDEERDecayData | Derived class that stores DEER decay data, either raw or background-corrected |
| CDEERDistanceBounds | Derived class for storing the data as a bounded function. Contains the upper and lower bounds, as well as steepness. If the average simulated distance falls within these bounds the score is zero If the average falls outside, it is evaluated via the steepness For example: ( ( lb - d ) / s ) ^2 OR ( ( d - ub ) / s ) ^2 lb: Lower bound ub: Upper bound d: Avg distance s: Steepness |
| CDEERDistanceDistribution | |
| CDEERIO | |
| CEPRSpinLabel | |
| CFittingInfo | Struct for fitting DEER traces. Copies are stored in each DEERDecayData object |
| CSimulated4PDEERTrace | |
| ►Netable | |
| ►Ncoulomb | |
| CCoulomb | |
| ►Ncount_pair | |
| CCountPair1B | |
| CCountPair2B | |
| CCountPairAll | |
| CCountPairCrossover3 | |
| CCountPairCrossover34 | |
| CCountPairCrossover3full | |
| CCountPairCrossover4 | |
| CCountPairFactory | |
| CCountPairFunction | |
| CCountPairGeneric | |
| CCountPairIntraRes | |
| CCountPairNone | |
| CInvoker | |
| ►Netrie | |
| CCountPairData_1_1 | |
| CCountPairData_1_2 | |
| CCountPairData_1_3 | |
| CCountPairDataGeneric | |
| CEtableAtom | |
| CGenericResidueConnectionData | |
| CTrieCountPair1BC3 | |
| CTrieCountPair1BC4 | |
| CTrieCountPairAll | |
| CTrieCountPairGeneric | |
| CTrieCountPairNone | |
| CAnalyticEtableEnergy | |
| CAnalyticEtableEvaluator | |
| CAtomPairEnergy | |
| CBaseEtableEnergy | |
| CBB_BB_EnergyInvoker | |
| CEtable | Class definition for Etable |
| CEtableClassicIntraEnergyCreator | |
| CEtableEnergyCreator | |
| CEtableEvaluator | |
| CEtableOptions | |
| CEtableParamsOnePair | EtableParamsOnePair describes all of the parameters for a particular pair of atom types necessary to evaluate the Lennard-Jones and LK solvation energies |
| CExtraQuadraticRepulsion | ExtraQuadraticRepulsion class is used to add in extra repulsion for particular atom pairs, if needed, (e.g. for OCbb/OCbb) where the functional form is: fa_rep += (xhi - x)^2 * slope for values of x between xlo and xhi, and fa_rep += (x - xlo ) * extrapolated_slope + ylo where extrapolated slope can be anything, but, to defined a function with continuous derivatives, should be extrapolated_slope = (xhi-xlo)^2*slope. This is the analytical implementation of the "modify_pot" behavior |
| CMembEtable | Table of pre-computed LK membrane solvation energies |
| CResResEnergyInvoker | |
| CSC_BB_EnergyInvoker | |
| CSC_SC_EnergyInvoker | |
| CSC_Whole_EnergyInvoker | |
| CTableLookupEtableEnergy | |
| CTableLookupEvaluator | |
| CWholeWholeEnergyInvoker | |
| ►Nfiber_diffraction | |
| CCentroidScatter | Silly vector1 wrapper class so we can derive from PoseCachedData |
| CFAScatter | Silly vector1 wrapper class so we can derive from PoseCachedData |
| CFiberDiffraction | |
| CFiberDiffractionEnergy | |
| CFiberDiffractionEnergyCreator | |
| CFiberDiffractionEnergyDens | |
| CFiberDiffractionEnergyDensCreator | |
| CHankel | |
| CKromerMann | |
| COneGaussianScattering | |
| ►Nfunc | |
| CAmberPeriodicFunc | Function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) |
| CCharmmPeriodicFunc | Function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) ) |
| CCircularGeneral1D_Func | Function that allows return of arbitrary FArrays – this time circularized |
| CCircularHarmonicFunc | Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints |
| CCircularPowerFunc | Generalization of CircularCircularPowerFunc – other exponents allowed |
| CCircularSigmoidalFunc | Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints |
| CCircularSplineFunc | |
| CConformationXYZ | |
| CConstantFunc | Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation |
| CCountViolFunc | |
| CEtableFunc | Class for representing arbitrarily defined functions |
| CFadeFunc | |
| CFlatHarmonicFunc | |
| CFourPointsFunc | 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 |
| CFunc | 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 |
| CFuncFactory | |
| CGaussianChainDoubleFunc | |
| CGaussianChainFunc | |
| CGaussianChainGeneralFunc | |
| CGaussianChainQuadrupleFunc | |
| CGaussianChainSingleFunc | |
| CGaussianChainTripleFunc | |
| CGaussianFunc | Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation |
| CHarmonicFunc | |
| CIdentityFunc | |
| CKarplusFunc | 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 |
| CLinearPenaltyFunction | |
| CMinMultiHarmonicFunc | |
| CMixtureFunc | 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 |
| CPeriodicFunc | Function of type y = ( k * cos(n * (x - x0) ) ) + C |
| CResiduePairXYZ | |
| CResidueXYZ | |
| CScalarWeightedFunc | |
| CSigmoidFunc | |
| CSkipViolFunc | |
| CSmoothStepFunc | |
| CSoedingFunc | Derived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation |
| CSOGFunc | Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation |
| CSOGFunc_Impl | Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation |
| CSplineFunc | |
| CSquareWell2Func | |
| CSquareWellFunc | |
| CSumFunc | |
| CTopOutFunc | |
| CUSOGFunc | Unnormalized, unbounded sum of Gaussians constraint |
| CXYZ_Func | Just a simple class that takes an AtomID and returns a Vector (position) |
| ►Ngeometric_solvation | |
| CContextDependentGeometricSolEnergy | |
| CContextDependentGeometricSolEnergyCreator | |
| CContextIndependentGeometricSolEnergy | |
| CContextIndependentGeometricSolEnergyCreator | |
| CDatabaseOccSolEne | |
| CExactOccludedHbondSolEnergy | |
| CExactOccludedHbondSolEnergyCreator | |
| CGeometricSolEnergyEvaluator | |
| CGridInfo | |
| COccludedHbondSolEnergy | |
| COccludedHbondSolEnergy_onebody | |
| COccludedHbondSolEnergy_onebodyCreator | |
| COccludedHbondSolEnergyCreator | |
| CWaterWeightGridSet | |
| ►Nhackaro | |
| CHackAroEnergy | |
| CHackAroEnergyCreator | |
| ►Nhbonds | |
| ►Ngraph | |
| CAtomInfo | |
| CAtomInfoSet | |
| CHBondEdge | Each HBondEdge represents a hydrogen bond |
| CHBondGraph | |
| CHBondInfo | |
| CHBondNode | Each HBondNode represents a rotamer from the RotamerSets object |
| CLKHBondInfo | |
| ►Nhbtrie | |
| CHBAtom | |
| CHBCountPairFunction | |
| CHBCPData | |
| CHBondsTrieVsTrieCachedDataContainer | A class for passing data to the trie-vs-trie calculation for hydrogen bonds, without having to cache it in mutable data in the HBondEnergy method or whatnot |
| CAssignmentScaleAndDerivVectID | Classes (that probably shouldn't be in here!!! ) /// |
| CFadeInterval | Classic FadeInterval |
| CHBDerivAssigner | |
| CHBEvalTuple | |
| CHBond | |
| CHBondDatabase | |
| CHBondDerivs | |
| CHBondEnergy | |
| CHBondEnergyCreator | |
| CHBondOptions | |
| CHBondResidueMinData | A class to hold data for the HBondEnergy class used in score and derivative evaluation |
| CHBondResPairMinData | |
| CHBondSet | A class that holds Hbond objects and helps setup Hbonds for scoring |
| CHBondTypeManager | |
| CNPDHBondEnergy | First pass implementation; somewhat ineffecient. The NPDHbondEnergy will cache a map of all hbonds by donor and acceptor in the Pose during setup_for_scoring, and will then retrieve these values during calls to residue_pair_energy. Doesn't work properly for packing |
| CNPDHBondEnergyCreator | |
| CNPDHBondSet | A class that holds Hbond objects and helps setup Hbonds for scoring |
| CPolynomial_1d | |
| CSSWeightParameters | Weights and Options /// |
| ►Ninterface_ | |
| CDDPlookup | |
| CDDPscore | |
| CDDPscoreCreator | |
| ►Nlkball | |
| ►Nlkbtrie | |
| CLKBAtom | |
| CLKBTrieEvaluator | |
| CLK_Ball_BB_BB_E_Invoker | |
| CLK_Ball_BB_SC_E_Invoker | |
| CLK_Ball_RPE_Invoker | |
| CLK_Ball_SC_SC_E_Invoker | |
| CLK_BallEnergy | |
| CLK_BallEnergyCreator | |
| CLK_BallInvoker | |
| CLKB_ResidueInfo | LKB_ResidueInfo holds the coordinates of the waters attached to a Residue |
| CLKB_ResiduesInfo | |
| CLKB_ResPairMinData | |
| CLKBallDatabase | A singleton class which stores data for LKBall terms. This is a separate singleton class, rather than static data on the LKB_ResidueInfo class so that the ResidueType destruction observer has a stable object to call back to |
| CScoredBridgingWater | |
| CWaterBuilder | |
| CWaterBuilderForRestype | |
| ►Nloop_graph | |
| ►Nevaluator | |
| CGaussianChainFuncPotentialEvaluator | |
| CLoopClosePotentialEvaluator | |
| CSixDTransRotPotential | |
| CSixDTransRotPotentialEvaluator | |
| Ccycle_printer | |
| CLoop | |
| CLoopCloseEnergy | |
| CLoopCloseEnergyCreator | |
| CLoopCycle | |
| CLoopGraph | |
| ►Nmagnesium | |
| CMgEnergy | |
| CMgEnergyCreator | |
| CMgKnowledgeBasedPotential | |
| CRNA_MgPointEnergy | |
| CRNA_MgPointEnergyCreator | |
| ►Nmembrane | |
| CFaMPEnvEnergy | Fullatom Membrane Environment Energy |
| CFaMPEnvEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| CFaMPEnvSmoothEnergy | Fullatom Membrane Solvation Energy - Statistically Derived, and smoothed derivatives |
| CFaMPEnvSmoothEnergyCreator | Membrane Termini Penalty Creator Class |
| CFaMPSolvEnergy | Energy Method: Membrane Fullaotm Solvation Energy (LK) |
| CFaMPSolvEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| CMembraneData | Mmebrane Data Class |
| CMPCbetaEnergy | Membrane Environemnt CBeta Energy Term |
| CMPCbetaEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| CMPEnvEnergy | Mmebrane Environemnt Energy Term |
| CMPEnvEnergyCreator | Creator Class for Membrane CBeta Energy Method |
| CMPHelicalityEnergy | Fullatom Membrane Solvation Energy - Statistically Derived, and smoothed derivatives |
| CMPHelicalityEnergyCreator | Membrane Termini Penalty Creator Class |
| CMPNonHelixPenalty | Class Membrane Non Helix Penalty |
| CMPNonHelixPenaltyCreator | Membrane Non Hleix in mmebrane Penalty Creator Class |
| CMPPairEnergy | Membrane Environemtn Residue Pair Energy Term |
| CMPPairEnergyCreator | Creator Class for Membrane Residue Pair Energy Method |
| CMPResidueLipophilicityEnergy | Fullatom Membrane Solvation Energy - Statistically Derived, and smoothed derivatives |
| CMPResidueLipophilicityEnergyCreator | Membrane Termini Penalty Creator Class |
| CMPSpanAngleEnergy | |
| CMPSpanAngleEnergyCreator | |
| CMPSpanInsertionEnergy | |
| CMPSpanInsertionEnergyCreator | |
| CMPTerminiPenalty | Class Membrane Termini Penalty |
| CMPTerminiPenaltyCreator | Membrane Termini Penalty Creator Class |
| CMPTMProjPenalty | Class Membrane TM proj Penalty |
| CMPTMProjPenaltyCreator | Membrane TM Proj Penalty Creator Class |
| ►Nmethods | |
| ►Ncarbohydrates | |
| CSugarBackboneEnergy | |
| CSugarBackboneEnergyCreator | EnergyMethodCreator allowing the ScoringManager to create a SugarBackboneEnergy method class |
| ►Ndfire | |
| CDFIRE_Energy | |
| CDFIRE_EnergyCreator | |
| CDFIRE_Potential | |
| CAbego | |
| CAbegoEnergyCreator | |
| CArgCationPiEnergy | |
| CArgCationPiEnergyCreator | |
| CAromaticBackboneRestraintEnergy | |
| CAromaticBackboneRestraintEnergyCreator | |
| CAspartimidePenaltyEnergy | |
| CAspartimidePenaltyEnergyCreator | |
| CBBDepCartBondedParameters | |
| CBBIndepCartBondedParameters | |
| CBranchEnergy | BranchEnergy class iterates across all residues in finalize() and determines a penalty between residues i and i+1 across a cutpoint by how much their virtual atoms do not align |
| CBranchEnergyCreator | |
| CBurial_v2Energy | |
| CBurial_v2EnergyCreator | |
| CBurialEnergy | |
| CBurialEnergyCreator | |
| CCartBondedParameters | |
| CCartesianBondedEnergy | |
| CCartesianBondedEnergyCreator | |
| CCenHBEnergy | |
| CCenHBEnergyCreator | |
| CCenPairEnergy | |
| CCenPairEnergyCreator | |
| CCenPairMotifDegreeEnergy | |
| CCenPairMotifDegreeEnergyCreator | |
| CCenPairMotifEnergy | |
| CCenPairMotifEnergyCreator | |
| CCenRotEnvEnergy | |
| CCenRotEnvEnergyCreator | |
| CCenRotPairEnergy | |
| CCenRotPairEnergyCreator | |
| CChainbreakEnergy | ChainbreakEnergy class iterates across all residues in finalize() and determines a penalty between residues i and i+1 across a cutpoint by how much their virtual atoms do not align |
| CChainbreakEnergyCreator | |
| CChemicalShiftAnisotropyEnergy | |
| CChemicalShiftAnisotropyEnergyCreator | |
| CContactOrderEnergy | |
| CContactOrderEnergyCreator | |
| CContextDependentLRTwoBodyEnergy | |
| CContextDependentOneBodyEnergy | |
| CContextDependentTwoBodyEnergy | |
| CContextIndependentLRTwoBodyEnergy | |
| CContextIndependentOneBodyEnergy | |
| CContextIndependentTwoBodyEnergy | |
| CCovalentLabelingEnergy | |
| CCovalentLabelingEnergyCreator | |
| CCovalentLabelingFAEnergy | |
| CCovalentLabelingFAEnergyCreator | |
| CCustomAtomPairEnergy | |
| CCustomAtomPairEnergyCreator | |
| CD2H_SA_Energy | |
| CD2H_SA_EnergyCreator | |
| CDipolarCouplingEnergy | |
| CDipolarCouplingEnergyCreator | |
| CDirectReadoutEnergy | Implementation of Kono and Sarai's knowledge-based protein-DNA interaction energy |
| CDirectReadoutEnergyCreator | |
| CDistanceChainbreakEnergy | 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 |
| CDistanceChainbreakEnergyCreator | |
| CDNA_BaseEnergy | |
| CDNA_BaseEnergyCreator | |
| CDNA_DihedralEnergy | |
| CDNA_DihedralEnergyCreator | |
| CDNA_EnvPairEnergy | Implementation of env and pair terms for protein-DNA interactions |
| CDNA_EnvPairEnergyCreator | |
| CDNA_ReferenceEnergy | |
| CDNA_ReferenceEnergyCreator | |
| CEnergyMethod | Base class for the energy method hierarchy |
| CEnergyMethodCreator | 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 |
| CEnergyMethodOptions | |
| CEnergyMethodRegistrator | 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 |
| CEnvEnergy | |
| CEnvEnergyCreator | |
| CEnvSmoothEnergy | |
| CEnvSmoothEnergyCreator | |
| CFa_MbenvEnergy | |
| CFa_MbenvEnergyCreator | |
| CFa_MbsolvEnergy | |
| CFa_MbsolvEnergyCreator | |
| CFACTSEnergy | |
| CFACTSEnergyCreator | |
| CFreeDOF_Energy | |
| CFreeDOF_EnergyCreator | |
| CFreeDOF_Options | |
| CGaussianOverlapEnergy | |
| CGaussianOverlapEnergyCreator | |
| CGenBornEnergy | |
| CGenBornEnergyCreator | |
| CGenericBondedEnergy | |
| CGenericBondedEnergyCreator | |
| CGoapEnergy | |
| CGoapEnergyCreator | |
| CGoapRsdType | |
| CHRF_MSLabelingEnergy | |
| CHRF_MSLabelingEnergyCreator | |
| CHybridVDW_Energy | |
| CHybridVDW_EnergyCreator | |
| CHydroxylTorsionEnergy | |
| CHydroxylTorsionEnergyCreator | |
| CIdealParametersDatabase | |
| CIntermolEnergy | |
| CIntermolEnergyCreator | |
| CLinearBranchEnergy | LinearBranchEnergy class iterates across all residues in finalize() and determines the penalty between branch-connected residues by how much their psueduo atoms do not align (if they have them) |
| CLinearBranchEnergyCreator | |
| CLinearChainbreakEnergy | 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 |
| CLinearChainbreakEnergyCreator | |
| CLK_hack | |
| CLK_hackCreator | |
| CLK_PolarNonPolarEnergy | |
| CLK_PolarNonPolarEnergyCreator | |
| CLK_SigmoidalFunc | |
| CLongRangeTwoBodyEnergy | |
| CMembraneCbetaEnergy | |
| CMembraneCbetaEnergyCreator | |
| CMembraneCenPairEnergy | |
| CMembraneCenPairEnergyCreator | |
| CMembraneEnvEnergy | |
| CMembraneEnvEnergyCreator | |
| CMembraneEnvPenalties | |
| CMembraneEnvPenaltiesCreator | |
| CMembraneEnvSmoothEnergy | |
| CMembraneEnvSmoothEnergyCreator | |
| CMembraneLipo | |
| CMembraneLipoCreator | |
| CMissingEnergy | |
| CMissingEnergyCreator | |
| CMMBondAngleEnergy | |
| CMMBondAngleEnergyCreator | |
| CMMBondLengthEnergy | |
| CMMBondLengthEnergyCreator | |
| CMMLJEnergyInter | |
| CMMLJEnergyInterCreator | |
| CMMLJEnergyIntra | |
| CMMLJEnergyIntraCreator | |
| CMMTorsionEnergy | |
| CMMTorsionEnergyCreator | |
| CMotifDockEnergy | |
| CMotifDockEnergyCreator | |
| CMultipoleElecEnergy | |
| CMultipoleElecEnergyCreator | |
| CMultipoleElecResPairMinData | |
| CNeighborListData | |
| CNMerPSSMEnergy | |
| CNMerPSSMEnergyCreator | |
| CNMerRefEnergy | |
| CNMerRefEnergyCreator | |
| CNMerSVMEnergy | |
| CNMerSVMEnergyCreator | |
| COmegaTetherEnergy | |
| COmegaTetherEnergyCreator | |
| COneBodyEnergy | |
| COtherPoseEnergy | |
| COtherPoseEnergyCreator | |
| CP_AA_Energy | |
| CP_AA_EnergyCreator | |
| CP_AA_pp_Energy | |
| CP_AA_pp_EnergyCreator | |
| CP_AA_ss_Energy | |
| CP_AA_ss_EnergyCreator | |
| CPackStatEnergy | |
| CPackStatEnergyCreator | |
| CPairEnergy | |
| CPairEnergyCreator | |
| CPBLifetimeCache | |
| CPeptideBondEnergy | 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 |
| CPeptideBondEnergyCreator | |
| CpHEnergy | |
| CpHEnergyCreator | |
| CPointWaterEnergy | |
| CPointWaterEnergyCreator | |
| CPoissonBoltzmannEnergy | |
| CPoissonBoltzmannEnergyCreator | |
| CProClosureEnergy | |
| CProClosureEnergyCreator | |
| CProQ_Energy | |
| CProQ_EnergyCreator | |
| CPyEnergyMethodRegistrator | 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 |
| CRamachandranEnergy | |
| CRamachandranEnergy2B | |
| CRamachandranEnergy2BCreator | |
| CRamachandranEnergyCreator | |
| CRamaPreProEnergy | |
| CRamaPreProEnergyCreator | |
| CReferenceEnergy | |
| CReferenceEnergyCreator | |
| CReferenceEnergyNoncanonical | |
| CReferenceEnergyNoncanonicalCreator | |
| CResidualDipolarCouplingEnergy | |
| CResidualDipolarCouplingEnergy_Rohl | |
| CResidualDipolarCouplingEnergy_RohlCreator | |
| CResidualDipolarCouplingEnergyCreator | |
| CResidueAtomOverlaps | |
| CResidueCartBondedParameters | |
| CRG_Energy_Fast | |
| CRG_Energy_FastCreator | |
| CRG_Local_MinData | |
| CRG_LocalEnergy | |
| CRG_LocalEnergyCreator | |
| CRG_MinData | |
| CRingClosureEnergy | |
| CRingClosureEnergyCreator | |
| CRMS_Energy | |
| CRMS_EnergyCreator | |
| CSA_Energy | |
| CSA_EnergyCreator | |
| CSASAEnergy | |
| CSASAEnergyCreator | |
| CSecondaryStructureEnergy | |
| CSecondaryStructureEnergyCreator | |
| CSequenceDependentRefEnergy | |
| CSequenceDependentRefEnergyCreator | |
| CShortRangeTwoBodyEnergy | |
| CSmoothCenPairEnergy | |
| CSmoothCenPairEnergyCreator | |
| CSmoothEnvEnergy | |
| CSmoothEnvEnergyCreator | |
| CSplitUnfoldedTwoBodyEnergy | |
| CSplitUnfoldedTwoBodyEnergyCreator | |
| CSSElementMotifContactEnergy | |
| CSSElementMotifContactEnergyCreator | |
| CSuckerEnergy | |
| CSuckerEnergyCreator | |
| CSymmetricLigandEnergy | |
| CSymmetricLigandEnergyCreator | |
| CTwoBodyEnergy | |
| CUnfoldedStateEnergy | |
| CUnfoldedStateEnergyCreator | |
| CVdWTinkerEnergy | |
| CVdWTinkerEnergyCreator | |
| CVdWTinkerResPairMinData | |
| CWaterAdductHBondEnergy | |
| CWaterAdductHBondEnergyCreator | |
| CWaterAdductIntraEnergy | |
| CWaterAdductIntraEnergyCreator | |
| CWaterSpecificEnergy | |
| CWaterSpecificEnergyCreator | |
| CWholeStructureEnergy | 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 |
| CYHHPlanarityEnergy | |
| CYHHPlanarityEnergyCreator | |
| ►Nmhc_epitope_energy | |
| CAlleleMatrix | The scoring matrix for one specific allele |
| CMHCEpitopeConstraint | |
| CMHCEpitopeEnergy | |
| CMHCEpitopeEnergyCreator | |
| CMHCEpitopeEnergySetup | MHCEpitopeEnergySetup, a helper class for the MHCEpitopeEnergy energy method that stores all of its setup data |
| CMHCEpitopePredictor | |
| CMHCEpitopePredictorExternal | |
| CMHCEpitopePredictorMatrix | An predictor based on a set of allele-specific profiles of which peptides are likely to be binders |
| CMHCEpitopePredictorPreLoaded | |
| CMHCEpitopePredictorSVM | |
| CScoreCache | A cache of epitope scores (considered and commited) at each position, to enable efficient updating of only those scores affected by a substitution during annealing |
| ►Nmm | |
| ►Nmmtrie | |
| CMMEnergyTableAtom | |
| CMMBondAngleLibrary | |
| CMMBondAngleResidueTypeParam | |
| CMMBondAngleResidueTypeParamSet | |
| CMMBondAngleScore | Calculates scores of mm bond angle paramater sets given an angle |
| CMMBondLengthLibrary | |
| CMMBondLengthScore | |
| CMMLJEnergyTable | Blah |
| CMMLJLibrary | A class to maintain a set of MM LJ paramaters |
| CMMLJScore | 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 |
| CMMTorsionLibrary | A class to maintain a set of MM torsion paramaters |
| CMMTorsionScore | Calculates scores of mm torsion paramater sets given an angle |
| ►Nmotif | |
| CMotifHash | |
| CMotifHashManager | |
| CMotifHit | |
| CMotifHits | |
| CMotifHitStats | |
| CMyHash | |
| CMyPred | |
| CResPairMotif | |
| CResPairMotifMetaBinner | |
| CResPairMotifQuery | |
| CResPairMotifs | |
| CRMSandEnergyCMP | |
| CRPM_FilterStats | |
| CXformScore | |
| CXformSummary | |
| CXfrag | |
| CXfragSet | |
| CXfres | |
| ►Nnetcharge_energy | |
| CNetChargeConstraint | |
| CNetChargeEnergy | NetChargeEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation |
| CNetChargeEnergyCreator | |
| CNetChargeEnergySetup | NetChargeEnergySetup, a helper class for the NetChargeEnergy energy method that stores all of its setup data |
| ►Nnmr | |
| ►Npcs | |
| CPCSData | |
| CPCSMultiSet | |
| CPCSSingle | |
| CPCSSingleSet | |
| CPCSTensor | |
| ►Npre | |
| CPREData | |
| CPREMultiSet | |
| CPRESingle | |
| CPRESingleSet | |
| ►Nrdc | |
| CRDCData | |
| CRDCMultiSet | |
| CRDCSingle | |
| CRDCSingleSet | |
| CRDCTensor | |
| CNMRDataFactory | |
| CNMRDummySpinlabelAtom | Derived class of VoxelGridPoint to store the 3D coordinates of one atom of a NMRDummySpinlabelConformer. NMRDummySpinlabelAtom is also a member of NMRDummySpinlabelConformer and holds a const pointer to its outer class |
| CNMRDummySpinlabelConformer | Class that stores information about one dummy spinlabel conformer (e.g. atom names and xyz coordinates, and whether it clashes with neighboring amino acid residues or not). A vector of NMRDummySpinlabelConformer objects is member of class NMRDummySpinlabelEnsemble |
| CNMRDummySpinlabelEnsemble | Class that represents a "dummy" spinlabel ensemble. It holds information about each individual conformer member (atom coordinates, number of observations) and data to score those based on atom clashes with the neighborhood of the ensemble. To speed up the clash score calculation, this class holds also an object of type NMRDummySpinlabelVoxelGrid which gets filled with constant pointers to NMRDummySpinlabelAtoms |
| CNMRDummySpinlabelVoxelGrid | Derived class of VoxelGrid to create a grid of VoxelGridPoint objects |
| CNMRGridSearch | |
| CNMRSpinlabel | |
| CNMRTensor | |
| CVoxelGridPoint | Base class of a point object from which the voxel grid is created |
| CVoxelGridPoint_AA | Derived class of VoxelGridPoint to store the 3D coordinates of one atom of an amino acid residue. In addition, it holds a const pointer to the residue object to which it refers to |
| ►Nnv | |
| CNVlookup | |
| CNVscore | |
| CNVscoreCreator | |
| ►Norbitals | |
| COrbitalsLookup | |
| COrbitalsScore | |
| COrbitalsScoreCreator | |
| COrbitalsStatistics | |
| ►Npacking | |
| CBall | |
| CHolesEnergy | |
| CHolesEnergyCreator | |
| CHolesEnergyRes | |
| CHolesParams | |
| CHolesParamsRes | |
| CHolesResult | Result class holding the three scores and the per-atom scores |
| CPoseBalls | |
| CPoseBallsLite | |
| CSurfEnergy | |
| CSurfEnergyCreator | |
| CSurfVol | |
| CSurfVolDeriv | |
| CSurfVolEnergy | |
| CSurfVolEnergyCreator | |
| ►Npackstat | |
| CAccumulator | |
| CAreaAccumulator | |
| CArray2D | |
| CAtomRadiusMap | |
| CCavityBall | |
| CCavityBallCluster | |
| CCircle | |
| CEvent | |
| CHTL_EventX | |
| CLeeRichards | |
| CLR_AtomData | |
| CLR_MP_AtomData | |
| CMultiProbePerSphereAccumulator | |
| CMultiProbePoseAccumulator | |
| COctree2D | |
| COrderCavBallOnR | |
| COrderCavBallOnRmAnb | |
| COrderCavBallOnRmE | |
| COrderCavBallOnX | |
| COrderCBC | |
| COrderSphereOnID | |
| COrderSphereOnX | |
| CPackingScore | |
| CPackingScoreResData | |
| CPerSphereAccumulator | |
| CPoint | |
| CPointPair | |
| CPosePackData | |
| CSasaOptions | |
| CSasaResult | |
| CSimplePDB | |
| CSimplePDB_Atom | |
| CSlice | |
| CSphere | |
| Ctrace | |
| ►Npower_diagram | |
| CPDinter | |
| CPDsphere | |
| CPDvertex | |
| CPowerDiagram | |
| CSAnode | |
| ►Nrna | |
| ►Nchemical_shift | |
| CChemicalShiftData | |
| CRNA_ChemicalShiftEnergy | |
| CRNA_ChemicalShiftEnergyCreator | |
| CRNA_ChemicalShiftPotential | |
| CRNA_CS_parameters | |
| CRNA_CS_residue_parameters | |
| ►Ndata | |
| CRNA_ChemicalMappingEnergy | |
| CRNA_ChemicalMappingEnergyCreator | |
| CRNA_DataBackboneEnergy | |
| CRNA_DataBackboneEnergyCreator | |
| CRNA_DMS_LowResolutionPotential | |
| CRNA_DMS_Potential | |
| CRG_Energy_RNA | |
| CRG_Energy_RNACreator | |
| CRNA_AtomVDW | |
| CRNA_BulgeEnergy | |
| CRNA_BulgeEnergyCreator | |
| CRNA_CentroidInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| CRNA_EnergyMethodOptions | |
| CRNA_FullAtomStackingEnergy | |
| CRNA_FullAtomStackingEnergyCreator | |
| CRNA_FullAtomVDW_BasePhosphate | |
| CRNA_FullAtomVDW_BasePhosphateCreator | |
| CRNA_JR_SuiteEnergy | |
| CRNA_JR_SuiteEnergyCreator | |
| CRNA_LJ_BaseEnergy | |
| CRNA_LJ_BaseEnergyCreator | |
| CRNA_LowResolutionPotential | |
| CRNA_LowResolutionPotentialCreator | |
| CRNA_Motif | |
| CRNA_Motifs | |
| CRNA_PairwiseLowResolutionEnergy | |
| CRNA_PairwiseLowResolutionEnergyCreator | |
| CRNA_PartitionEnergy | |
| CRNA_PartitionEnergyCreator | |
| CRNA_ScoringInfo | Keep track of RNA centroid, useful atom, base-base info inside the pose |
| CRNA_StubCoordinateEnergy | |
| CRNA_StubCoordinateEnergyCreator | |
| CRNA_SugarCloseEnergy | |
| CRNA_SugarCloseEnergyCreator | |
| CRNA_SuiteEnergy | |
| CRNA_SuiteEnergyCreator | |
| CRNA_SuitePotential | |
| CRNA_TorsionEnergy | |
| CRNA_TorsionEnergyCreator | |
| CRNA_TorsionPotential | |
| CRNA_VDW_Energy | |
| CRNA_VDW_EnergyCreator | |
| CRNP_LowResEnergy | |
| CRNP_LowResEnergyCreator | |
| CRNP_LowResPairDistEnergy | |
| CRNP_LowResPairDistEnergyCreator | |
| CRNP_LowResPairDistPotential | |
| CRNP_LowResPotential | |
| CRNP_LowResStackData | |
| CRNP_LowResStackEnergy | |
| CRNP_LowResStackEnergyCreator | |
| CStackElecEnergy | |
| CStackElecEnergyCreator | |
| CTNA_SuiteEnergy | |
| CTNA_SuiteEnergyCreator | |
| CTNA_SuitePotential | |
| ►Nsasa | |
| CLeGrandSasa | LeGrand SASA approximation method Used by SasaCalc but can be used by itself. Virt atms are skipped as radii=0 |
| CSasaCalc | Main interface to sasa calculations outside of pose metrics. Virt atms are skipped as radii=0 |
| CSasaMethod | Abstract base class for SasaMethods. Feel free to edit as needed. Virt atms are skipped as radii=0 |
| ►Nsaxs | |
| CDistanceHistogram | |
| CFastSAXSEnergy | |
| CFastSAXSEnergyCreator | |
| CFormFactor | |
| CFormFactorManager | Selects a given number of fragments using a quota scheme |
| CSAXSEnergy | |
| CSAXSEnergyCEN | |
| CSAXSEnergyCreator | |
| CSAXSEnergyCreatorCEN | |
| CSAXSEnergyCreatorFA | |
| CSAXSEnergyFA | |
| CSinXOverX | |
| ►Nsc | |
| C_ATOM_RADIUS | |
| C_DOT | |
| C_PROBE | |
| C_RESULTS | |
| CAtom | |
| CCloserToAtom | A small struct to report which of two atoms is closer to a given atom: |
| CContactMolecularSurfaceCalculator | |
| CElectrostaticComplementarityCalculator | |
| CElectrostaticComplementarityResults | |
| CMolecularSurfaceCalculator | |
| CShapeComplementarityCalculator | |
| CShapeComplementarityCalculatorException | |
| ►Nsolid_surface | |
| CSurfaceEnergies | |
| ►Nsym_e | |
| CsymECreator | |
| CsymEnergy | |
| ►Nsymmetry | |
| CSymmetricEnergies | |
| CSymmetricScoreFunction | This class is provided as a backward compatibility shim At this point it should be identical to the base ScoreFunction |
| ►Ntrie | |
| CCPDataCorrespondence | |
| CRotamerDescriptor | |
| CRotamerDescriptorAtom | |
| CRotamerTrie | |
| CRotamerTrieBase | |
| CTrieCollection | |
| CTrieCountPairBase | |
| CTrieNode | |
| CTrieVsTrieCachedDataContainerBase | A generic base class for passing data to the trie-vs-trie calculation, without having to cache it in mutable data in an EnergyMethod or whatnot |
| ►Nutil_methods | |
| CDumpTrajectoryEnergy | DumpTrajectoryEnergy, a util_method that allows one to dump rosetta trajectories through the use of the dump_trajectory ScoreType |
| CDumpTrajectoryEnergyCreator | |
| ►Nvdwaals | |
| CVDW_Energy | |
| CVDW_EnergyCreator | |
| CVDWAtom | |
| CVDWTrieCountPair1B | |
| CVDWTrieEvaluator | |
| ►CAPBSConfig | |
| CI_PARAM | |
| CR_PARAM | |
| CAPBSResult | |
| CAPBSWrapper | |
| CAtomNeighbor | Atom-atom neighborlist object |
| CAtomVDW | |
| CBB_Pos | |
| CBondOrderParser | |
| CCenHBPotential | |
| CCenListInfo | Keep track of the cenlist information |
| CCenRotEnvPairPotential | |
| CChemicalShiftAnisotropy | 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 |
| CContextGraph | |
| CContextGraphFactory | |
| CCSA | |
| Cdata_struct | |
| CDC | |
| CDenseEnergyContainer | |
| CDenseNeighborConstIterator | |
| CDenseNeighborIterator | |
| CDerivVectorPair | A glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms |
| CDimerPairing | |
| CDipolarCoupling | 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 |
| CDockingScoreFunction | |
| CEMapVector | A vector for storing energy data, initially all values are 0 |
| CEnergies | A cached energies object |
| CEnergyEdge | |
| CEnergyGraph | 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 |
| CEnergyNode | |
| CEnvPairPotential | |
| CExcludedResPredicate | |
| CFACTSPoseInfo | |
| CFACTSPotential | |
| CFACTSResidueInfo | |
| CFACTSRotamerSetInfo | |
| CFACTSRsdTypeInfo | |
| CFACTSRsdTypeMap | The FACTSRsdTypeMap is a collection of FACTSRsdTypeInfo for a number of residue types (This is a separate class to shield the raw pointer usage here |
| CGenBondedExclInfo | |
| CGenBornPoseInfo | |
| CGenBornPotential | |
| CGenBornResidueInfo | |
| CGenBornRotamerSetInfo | |
| CGenericBondedPotential | Potential for core/scoring/methods/GenericBondedEnergy method |
| CGenTorsionParams | Parameter set for one torsion angle |
| CHairpin | |
| CHairpins | |
| CHelices | |
| CHydroxylTorsionPotential | |
| CIsMainAtomPredicate | |
| CIsProteinCAPredicate | |
| CLREnergyContainer | |
| CMembrane_FAEmbed | Membrane Fullatom embedding info |
| CMembrane_FAPotential | Mmebrane Fullatom Potential - Scoring Class |
| CMembraneEmbed | Whole Pose Membrane Embedding |
| CMembranePotential | Rosetta Membrane Low Resolution Scoring Methods |
| CMembraneTopology | |
| CMinimizationEdge | |
| CMinimizationGraph | 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 |
| CMinimizationNode | |
| CMinScoreScoreFunction | |
| CMultipoleElecPoseInfo | |
| CMultipoleElecPotential | |
| CMultipoleElecResidueInfo | |
| CMultipoleElecRotamerSetInfo | |
| CMultipoleParameter | |
| CNeighborList | |
| COmegaTether | |
| COneToAllEnergyContainer | |
| COneToAllNeighborConstIterator | |
| COneToAllNeighborIterator | |
| CP_AA | |
| CP_AA_ABEGO3 | |
| CP_AA_ss | |
| CPairEPotential | |
| CPDatom | |
| CPDinter | |
| CPDvertex | |
| CPointWaterPotential | |
| CPoissonBoltzmannPotential | |
| CPolymerBondedEnergyContainer | |
| CPolymerBondedNeighborConstIterator | |
| CPolymerBondedNeighborIterator | |
| CPQR | |
| CPredicate | |
| CProQPotential | |
| CRamachandran | |
| CRamachandran2B | |
| CRamaPrePro | |
| CRDC | |
| CRDC_Rohl | |
| CResidualDipolarCoupling | 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 |
| CResidualDipolarCoupling_Rohl | |
| CResidueExclParams | |
| CResidueNblistData | |
| CResidueNeighborConstIterator | |
| CResidueNeighborIterator | |
| CResiduePairNeighborList | |
| CResPairMinimizationData | |
| CResRangePredicate | |
| CResSingleMinimizationData | |
| CSAnode | |
| CSASAPotential | |
| CScoreFunction | 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 |
| CScoreFunctionFactory | A collection of functions for making a single score_function |
| CScoreFunctionInfo | Info on the scorefunction settings |
| CScoreTypeManager | |
| CScoringManager | |
| CSecondaryStructurePotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| CSecondaryStructureWeights | Holds weights and flags for configuring a SecondaryStructureEnergy evaluation |
| CSelectedResPredicate | |
| CSigmoidWeightedCenList | Keep track of the cenlist information stores both centroid counts (T = Real) as well as d_centroid_counts (T = Vector) |
| CSmallAtNb | |
| CSmoothEnvPairPotential | |
| CSmoothScoreTermCoeffs | |
| CSplitUnfoldedTwoBodyPotential | |
| CSpringParams | Parameter set for one torsion angle |
| CSS_Info | |
| CSS_Killhairpins_Info | |
| CStrands | |
| CtableID | |
| CTenANeighborEdge | |
| CTenANeighborGraph | |
| CTenANeighborNode | |
| CTMscore | |
| CTMscoreStore | |
| CTorsionParams | |
| CTwelveANeighborEdge | |
| CTwelveANeighborGraph | |
| CTwelveANeighborNode | |
| CUnfoldedStatePotential | |
| CVdWTinkerPoseInfo | |
| CVdWTinkerPotential | |
| CVdWTinkerResidueInfo | |
| CVdWTinkerRotamerSetInfo | |
| CWaterAdductHBondPotential | |
| ►Nselect | |
| ►Njump_selector | |
| CAndJumpSelector | The AndJumpSelector combines the output of multiple JumpSelectors using AND logic, i.e., only jumps selected by ALL contained JumpSelectors will be selected. JumpSelecters can be pulled in from a DataMap, from subtags (for JumpSelectors known to the JumpSelectorFactory) or programmatically through add_jump_selector |
| CAndJumpSelectorCreator | |
| CInterchainJumpSelector | The InterchainJumpSelector returns a JumpSubset, i.e. a utility::vector1< bool > containing 'true' for jump where the take-off residue is on a different chain from the landing residue |
| CInterchainJumpSelectorCreator | |
| CJumpIndexSelector | The JumpIndexSelector returns a JumpSubset, i.e. a utility::vector1< bool > containing 'true' for jump positions which lie upstream of a given jump in the FoldTree. The jump is specified by its integer index |
| CJumpIndexSelectorCreator | |
| CJumpSelector | |
| CJumpSelectorCreator | |
| CJumpSelectorFactory | |
| CJumpSelectorRegistrator | This templated class will register an instance of an JumpSelectorCreator (class T) with the JumpSelectorFactory. It will ensure that no JumpSelector creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CNotJumpSelector | The NotJumpSelector negates the input of one loaded JumpSelector, i.e., it is a logical NOT - it selects all unselected jumps and deselects the selected ones. True becomes false, false becomes true. The JumpSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for JumpSelectors known to the JumpSelectorFactory or programmatically using set_jump_selector. Note that since most JumpSelectors clear the input JumpSubset, NOT can be thought of as simply selecting the opposite of the passed in selector |
| CNotJumpSelectorCreator | |
| COrJumpSelector | The OrJumpSelector combines the output of multiple JumpSelectors using OR logic, i.e., jumps selected by ANY of the contained JumpSelectors will be selected. JumpSelectors can be pulled in from a DataMap, from subtags (for JumpSelectors known to the JumpSelectorFactory) or programmatically through add_jump_selector |
| COrJumpSelectorCreator | |
| ►Nmovemap | |
| ►CMoveMapFactory | |
| CMMJumpAction | An action for a set of Jumps |
| CMMResAction | An action to be applied to a residue all members of a particular part (i.e. all backbone torsions, or all chi torsions) |
| CMMResIndexAction | An action for a particular indexed thing (i.e. a particular backbone, or a particular chi torsion) |
| ►Nresidue_selector | |
| CAndResidueSelector | The AndResidueSelector combines the output of multiple ResidueSelectors using AND logic, i.e., only residues selected by ALL contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through add_residue_selector |
| CAndResidueSelectorCreator | |
| CAsymmetricUnitSelector | A residue selector for selecting the master subunit in a symmetrical pose. If not symmetrical, will select the whole pose |
| CAsymmetricUnitSelectorCreator | |
| CBinSelector | A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin) |
| CBinSelectorCreator | |
| CBondedResidueSelector | The BondedResidueSelector selects residues that are connected to some set of residues (input_set) by a chemical bond. The input_set can be directly set using a set of residue positions or by a ResidueSelector |
| CBondedResidueSelectorCreator | |
| CCachedResidueSubset | |
| CChainSelector | |
| CChainSelectorCreator | |
| CCloseContactResidueSelector | A class that finds the neighboring residues for a particular residue by looking at atom-atom distances |
| CCloseContactResidueSelectorCreator | |
| CDensityFitResidueSelector | Selects residues that are considered 'error' region with respect to the density resolution |
| CDensityFitResidueSelectorCreator | |
| CFalseResidueSelector | |
| CFalseResidueSelectorCreator | |
| CGlycanLayerSelector | A selector for choosing glycan residues based on their layer - as measured by the residue distance to the start of the glycan tree. If no layer is set, will select all glycan residues |
| CGlycanLayerSelectorCreator | |
| CGlycanPositionSelector | A Residue Selector for selecting specific parts of arbitrary glycans by 'position' |
| CGlycanPositionSelectorCreator | |
| CGlycanResidueSelector | A ResidueSelector for carbohydrates and individual carbohydrate trees. Selects all Glycan residues if no option is given or the branch going out from the root residue. Selecting from root residues allows you to choose the whole glycan branch or only tips, etc |
| CGlycanResidueSelectorCreator | |
| CGlycanSequonsSelector | Find glycosylation sequons in pose Glycosylation sites are typically recognized by enzymes by means of a recognition sequence, or 'motif'. This ResidueSelector selects all residues that can be glycosylated using one of a few sequence motifs that are pre-defined and can be selected. For selecting residues in other motifs, use the ResidueInSequenceMotifSelctor, which takes regular expressions as input |
| CGlycanSequonsSelectorCreator | |
| CInterGroupInterfaceByVectorSelector | The InterGroupInterfaceByVectorSelector identifies residues at the interface between two groups of residues using two distance cutoffs: the first, shorter cutoff is based on atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the residues in the first group point toward the c-alphas of the other group. Each group may be specified either explicitly through a std::set of residue indices, through a string of comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue 13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset |
| CInterGroupInterfaceByVectorSelectorCreator | |
| CJumpDownstreamSelector | The JumpDownstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which lie downstream of a given jump in the FoldTree. The jump is specified by an integer index |
| CJumpDownstreamSelectorCreator | |
| CJumpUpstreamSelector | The JumpUpstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which lie upstream of a given jump in the FoldTree. The jump is specified by its integer index |
| CJumpUpstreamSelectorCreator | |
| CLayerSelector | The LayerSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally |
| CLayerSelectorCreator | |
| CNeighborhoodResidueSelector | The NeighborhoodResidueSelector selects residues neighboring a defined set of residues (the focus). The focus residue set can be obtained from another ResidueSelector, from a set of positions. Focus is included in subset by default. Use include_focus_in_subset to change this! |
| CNeighborhoodResidueSelectorCreator | |
| CNotResidueSelector | The NotResidueSelector negates the input of one loaded ResidueSelector, i.e., it is a logical NOT - it selects all unselected residues and deselects the selected ones. True becomes false, false becomes true. The ResidueSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for ResidueSelectors known to the ResidueSelectorFactory or programmatically using set_residue_selector. Note that since most ResidueSelectors clear the input ResidueSubset, NOT can be thought of as simply selecting the opposite of the passed in selector |
| CNotResidueSelectorCreator | |
| CNumNeighborsSelector | |
| CNumNeighborsSelectorCreator | |
| COrResidueSelector | The OrResidueSelector combines the output of multiple ResidueSelectors using OR logic, i.e., residues selected by ANY of the contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through add_residue_selector |
| COrResidueSelectorCreator | |
| CPhiSelector | A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences) |
| CPhiSelectorCreator | |
| CPrimarySequenceNeighborhoodSelector | The PrimarySequenceNeighborhoodSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are located near the given selected residues in primary sequence space |
| CPrimarySequenceNeighborhoodSelectorCreator | |
| CRandomGlycanFoliageSelector | Selects a random carbohydrate residue from a subset or selector, then selects the rest of the glycan foliage. Used for sampling |
| CRandomGlycanFoliageSelectorCreator | |
| CRandomResidueSelector | The RandomResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for N randomly selected residue positions, where N is a user-specified integer |
| CRandomResidueSelectorCreator | |
| CResidueIndexSelector | The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). It can also take range specifications (e.g. 10A-20A). Detection and mapping from PDB to Rosetta residue numbers is done internally |
| CResidueIndexSelectorCreator | |
| CResidueInMembraneSelector | The ResidueInMembraneSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are either in or out of the membrane. default is in |
| CResidueInMembraneSelectorCreator | |
| CResidueInSequenceMotifSelector | Select residues by motif search This selector takes a regular expression and a position and then finds all matches of the regular expression and selects the n-th residue in each match, where 'n' is the specified position |
| CResidueInSequenceMotifSelectorCreator | |
| CResidueNameSelector | The ResidueNameSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally |
| CResidueNameSelectorCreator | |
| CResiduePDBInfoHasLabelSelector | The ResiduePDBInfoHasLabelSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions with the given label in pose PDB info for that residue |
| CResiduePDBInfoHasLabelSelectorCreator | |
| CResiduePropertySelector | A residue selector that selects based on set residue properties |
| CResiduePropertySelectorCreator | |
| CResidueRange | Class for storing a range of resids |
| CResidueRanges | |
| CResidueSelector | |
| CResidueSelectorCreator | |
| CResidueSelectorFactory | |
| CResidueSelectorRegistrator | This templated class will register an instance of an ResidueSelectorCreator (class T) with the ResidueSelectorFactory. It will ensure that no ResidueSelector creator is registered twice, and centralizes this registration logic so that thread safety issues can be handled in one place |
| CResidueSpanSelector | The ResidueSpanSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are within a given span. A span is defined by start and end point, each as either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally. (The span is defined based on Rosetta indicies, even if residues are given by PDB numbers.) |
| CResidueSpanSelectorCreator | |
| CResidueVector | |
| CReturnResidueSubsetSelector | A simple selector that returns the set subset. This is to enable simplification of code-based interfaces to residue selectors, so that one may accept only selectors, but using this selector, we can set subsets |
| CScoreTermValueBasedSelector | |
| CScoreTermValueBasedSelectorCreator | |
| CSecondaryStructureSelector | |
| CSecondaryStructureSelectorCreator | |
| CSelectorLogicParser | Class to traverse the abstract syntax tree produced by the parsing of a properly-formed string in the Arithmetic expression language. Produces a ResidueSelector tree capable of logically joining together already-defined ResidueSelectors |
| CSliceResidueSelector | The SliceResidueSelector allows slicing of the returned values of other residue selectors |
| CSliceResidueSelectorCreator | |
| ►CSSElementSelector | The SSElementSelector allows you to select objects based on their secondary structure defintion. Language: "A,B,C" or "A,B", "c_term","n_term","middle" A = numerical position of THAT type of secondary structure. So if the secondary structure was Helix-Sheet-Helix. 2,H would refer to the second helix A could be positive or negative depending if you're counting from the n_term(positive) or c_term negative B = secondary structure type as assigned by DSSP , "H","E","L" C = S=Start, E=End, M=Middle |
| CSSElement | |
| CSSElementSelectorCreator | |
| CSymmetricalResidueSelector | The SymmetricalResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are symmetrically generated residues of the input list. (IE Union) |
| CSymmetricalResidueSelectorCreator | |
| CTrueResidueSelector | |
| CTrueResidueSelectorCreator | |
| ►Nutil | |
| CSelectResiduesByLayer | |
| CEnumerate1WithSelector | |
| CPreSelectedResidRange | |
| ►Nsequence | |
| CABEGO | Abego elments |
| CABEGOManager | Manager for abego |
| CAligner | |
| CAlignerFactory | |
| CAnnotatedSequence | |
| CBlosum62Map | |
| CCell | |
| CCharPairHash | |
| CChemicalShiftScoringScheme | |
| CChemicalShiftSequence | |
| CChemicalShiftSequenceCreator | |
| CCompassScoringScheme | |
| CCompositeScoringScheme | |
| CCompositeSequence | |
| CCompositeSequenceCreator | |
| CDerivedSequenceMapping | This is quite possibly the laziest form of class naming ever. What does the name of this class tell you about it? It's a SequenceMapping, and it's derived from SequenceMapping. Oops, it said it twice. What is different about this sequence mapping from the parent class? Who knows! When should you use it? Who knows!</snark> |
| CDP_Matrix | |
| CDPScoringScheme | |
| CL1ScoringScheme | |
| CLine | Struct |
| CMatrixScoringScheme | |
| CMCAligner | |
| CNWAligner | |
| CPairScoringScheme | |
| CProfSimScoringScheme | |
| CScoringScheme | |
| CScoringSchemeFactory | |
| CSequence | |
| CSequenceAlignment | |
| CSequenceAlignmentHasher | |
| CSequenceCoupling | |
| CSequenceCouplingCreator | |
| CSequenceCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| CSequenceFactory | |
| CSequenceProfile | |
| CSequenceProfileCreator | |
| CSequenceRegistrator | 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 |
| CSimpleScoringScheme | |
| CSimpleSequenceCreator | |
| CSSManager | Struct |
| CSWAligner | |
| ►Nsimple_metrics | |
| ►Ncomposite_metrics | |
| CCompositeEnergyMetric | A metric to report/calculate all of the energies of a scorefunction that are not 0 or the delta of each energy between another input pose |
| CCompositeEnergyMetricCreator | |
| CElectrostaticComplementarityMetric | |
| CElectrostaticComplementarityMetricCreator | |
| CEXCN_CalcFailed | Super-simple exception to be thrown when the EC calculator fails to compute |
| CEXCN_InitFailed | Super-simple exception to be thrown when we can't initialize the EC calculator |
| CProtocolSettingsMetric | This Metric reports options that have been set in the command line and splits script_vars. Each option name is the type and the setting is the value in the map. This is primarily aimed at benchmarking and record-keeping for large-scale rosetta runs or experiments. It works with both the global and local OptionsCollection to enable its use in JD3. It is analogous to the ProtocolFeatures reporter, with more options for xml-based variables |
| CProtocolSettingsMetricCreator | |
| ►Nmetrics | |
| CDihedralDistanceMetric | A metric to calculate the dihedral distance between two poses. Can set a subset of residues to calculate via ResidueSelector |
| CDihedralDistanceMetricCreator | |
| CInteractionEnergyMetric | Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions. Pose should be scored! |
| CInteractionEnergyMetricCreator | |
| CResidueSummaryMetric | A SimpleMetric that takes a PerResidueRealMetric and calculates different summaries of the overall data |
| CResidueSummaryMetricCreator | |
| CRMSDMetric | A metric to calculate the RMSD between two poses. Can set a subset of residues to calculate via ResidueSelector |
| CRMSDMetricCreator | |
| CSasaMetric | A Metric to cacluate overall sasa of a pose |
| CSasaMetricCreator | |
| CSecondaryStructureMetric | A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector. Uses DSSP |
| CSecondaryStructureMetricCreator | |
| CSelectedResidueCountMetric | A SimpleMetric that counts the number of residues in a residue selection |
| CSelectedResidueCountMetricCreator | |
| CSelectedResiduesMetric | Output residue-selected residues to a score file as rosetta resnums or pdbnums |
| CSelectedResiduesMetricCreator | |
| CSelectedResiduesPyMOLMetric | A utility metric to output a string of selected residues from a residue selector as a pymol selection |
| CSelectedResiduesPyMOLMetricCreator | |
| CSequenceMetric | A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector |
| CSequenceMetricCreator | |
| CSequenceSimilarityMetric | Compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62 |
| CSequenceSimilarityMetricCreator | |
| CTimingProfileMetric | Calculate the time difference between construction and apply/calculate. Useful to time protocols in RosettaScripts or through mover containers |
| CTimingProfileMetricCreator | |
| CTotalEnergyMetric | A metric to report the total energy of the system or the delta total energy between another input pose |
| CTotalEnergyMetricCreator | |
| ►Nper_residue_metrics | |
| CHbondMetric | A metric to report the total h-bonds residues from a selection to all [OTHER] residues, or from a set of residues to another set of residues. If No selection is given, will report ALL vs ALL |
| CHbondMetricCreator | |
| CPerResidueClashMetric | A SimpleMetric that calculates the total number of atom-atom clashes from a residue in a residue selector to all other residues defined in a second residue selector using the LJ radius of each atom |
| CPerResidueClashMetricCreator | |
| CPerResidueDensityFitMetric | A per-residue metric that will calculate the density fit for each residue using either a correlation or a zscore |
| CPerResidueDensityFitMetricCreator | |
| CPerResidueEnergyMetric | A per-residue metric that will calculate/output per residue total energies or a specific score component. WEIGHTED. Correctly decomposes energies to per-residue |
| CPerResidueEnergyMetricCreator | |
| CPerResidueGlycanLayerMetric | A metric that outputs the layer of the glycan tree as measured by the residue distance to the root |
| CPerResidueGlycanLayerMetricCreator | |
| CPerResidueRMSDMetric | A per-residue metric thtat will calculate the RMSD for each residue given in a residue selector to a reference pose |
| CPerResidueRMSDMetricCreator | |
| CPerResidueSasaMetric | A per-residue metric that will calculate SASA for each residue given in a selector |
| CPerResidueSasaMetricCreator | |
| CWaterMediatedHbondMetric | A metric to measure hydrogen bonds between a set of residues that are water-mediated |
| CWaterMediatedHbondMetricCreator | |
| CCompositeRealMetric | A class that is derived to calculate a set of core::Real values. Apply(pose) method calculates this metric and adds it to the pose score for output |
| CCompositeStringMetric | A class that is derived to calculate a set of string values. Apply(pose) method calculates this metric and adds it to the pose score for output |
| CMetricKey | The key needed to set data in our SimpleMetricData. This allows only SimpleMetrics to set data |
| CPerResidueRealMetric | A class that is derived to calculate a set of core::Real values for each Residue. Apply(pose) method calculates this metric and adds it to the pose score for output |
| CPerResidueStringMetric | A class that is derived to calculate a set of string values. Apply(pose) method calculates this metric and adds it to the pose score for output |
| CRealMetric | A class that is derived to calculate a Real (float) value |
| CSimpleMetric | The base class for Metrics in the Metric/Filter/Reporter system |
| CSimpleMetricCreator | |
| CSimpleMetricData | A container class for all Simple Metrics stored in the pose |
| CSimpleMetricFactory | |
| CSimpleMetricRegistrator | This templated class will register an instance of an SimpleMetricCreator (class T) with the SimpleMetricFactory. It will ensure that no SimpleMetric creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CSimpleMetricStruct | Structure for all SimpleMetric Data. Used for mmTF IO and multistage protocols |
| CStringMetric | A class that is derived to calculate a string value |
| CTestCompositeRealMetric | |
| CTestCompositeRealMetricCreator | |
| CTestCompositeStringMetric | |
| CTestCompositeStringMetricCreator | |
| CTestPerResidueRealMetric | |
| CTestPerResidueRealMetricCreator | |
| CTestPerResidueStringMetric | |
| CTestPerResidueStringMetricCreator | |
| CTestRealMetric | |
| CTestRealMetricCreator | |
| CTestStringMetric | Create subclasses for each type of metric |
| CTestStringMetricCreator | |
| ►Nutil | |
| CChainbreakUtil | |
| ►Ndevel | |
| ►NObjexxFCL | Application level code for relax-type protocols |
| ►Nprotocols | The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP |
| ►Naa_composition | |
| CAddCompositionConstraintMover | |
| CAddCompositionConstraintMoverCreator | |
| CAddHelixSequenceConstraintsMover | This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues |
| CAddHelixSequenceConstraintsMoverCreator | |
| CAddMHCEpitopeConstraintMover | |
| CAddMHCEpitopeConstraintMoverCreator | |
| CAddNetChargeConstraintMover | |
| CAddNetChargeConstraintMoverCreator | |
| CClearCompositionConstraintsMover | |
| CClearCompositionConstraintsMoverCreator | |
| ►Nabinitio | |
| ►Nabscript | |
| CAbscriptLoopCloserCM | |
| CAbscriptLoopCloserCMCreator | |
| ►CAbscriptMover | |
| CStageTracker | |
| CAbscriptMoverCreator | |
| CAbscriptStageMover | |
| CAtomPack | |
| CConstraintPreparer | |
| CConstraintPreparerCreator | |
| CFragmentCM | |
| CFragmentCMCreator | |
| CFragmentJumpCM | |
| CFragmentJumpCMCreator | |
| CJumpSampleData | |
| CJumpSampleDataCreator | |
| CResidueChunkSelection | |
| CRigidChunkCM | |
| CRigidChunkCMCreator | |
| CStagePreparer | |
| CStructPerturberCM | |
| CStructPerturberCMCreator | |
| C_HashEntry | |
| C_MergableEntries | |
| CAbrelaxApplication | Application level code for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT |
| CAbrelaxMover | |
| CAllResiduesChanged | (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values |
| CAlternativePairings | |
| CClassicAbinitio | |
| CComputeTotalDistCst | |
| CConstraintFragmentSampler | |
| CCoordinateConstraintKC | |
| CDomainAssembly | Insert fragments in a linker region. Very similar to what's in looprelax_main |
| CDomainAssemblyCreator | |
| CDoubleLayerKinematicAbinitio | |
| CFixTemplateJumpSetup | |
| CFoldConstraints | 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() |
| CFragmentSampler | |
| ChConvergenceCheck | |
| CHedgeArchive | |
| CIterativeAbrelax | |
| CIterativeBase | |
| CIterativeCentroid | |
| CIterativeFullatom | |
| CJumpingFoldConstraintsWrapper | |
| CKinematicAbinitio | |
| CKinematicControl | |
|
