 |
Rosetta
3.8
|
|
Rosetta
3.8
|
| ►Nboost | |
| ►Ncore | A class for reading in the atom type properties |
| ►Nchemical | |
| ►Ncarbohydrates | |
| CCarbohydrateInfo | |
| CCarbohydrateInfoManager | |
| CLinkageConformerData | Holds original conformer data from GlycanRelax |
| 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 | |
| CPeptoidRotamerLibrarySpecification | |
| CPeptoidRotamerLibrarySpecificationCreator | |
| 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) |
| 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 |
| 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) |
| CReplaceMainchainAtom | Replace a mainchain atom |
| CReplaceProtonWithBromine | Replace proton with bromine |
| CReplaceProtonWithChlorine | Replace proton with chlorine |
| CReplaceProtonWithEthyl | Replace proton with methyl |
| CReplaceProtonWithFluorine | Replace proton with fluorine |
| CReplaceProtonWithHydroxyl | Replace proton with hydroxyl |
| CReplaceProtonWithIodine | Replace proton with iodine |
| CReplaceProtonWithMethoxy | Replace proton with methyl |
| 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 | |
| CResidueLoader | |
| CResidueLoaderCreator | |
| CResidueLoaderOptions | |
| CResidueLoaderOptionsCreator | |
| CResidueProperties | |
| CResidueType | A class for defining a type of residue |
| 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 | |
| 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_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_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 to 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_POSITION | Does the main chain of this residue follow from the given position label? |
| CSelector_VARIANT_TYPE | Does the residue have ANY of variant types? |
| 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 |
| 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 |
| CSetOrientAtom | Set orient atom selection mode |
| CSetPolymerConnectAtom | Set an atom as polymer connection |
| CSetVirtualShadow | Set virtual shadow atoms |
| CVirtualizeAll | Virtualize all |
| ►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 |
| ►Nmembrane | |
| CEXCN_Illegal_Arguments | Illegal Arguments Exception |
| 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 |
| CLipidAccInfo | Membrane Lipid Accessibility Data |
| CMembraneInfo | MembraneInfo describes the membrane bilayer and its relationship with the protein |
| CSpan | |
| CSpanningTopology | |
| ►Norbitals | |
| COrbitalXYZCoords | |
| ►Nparametric | |
| 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 |
| ►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 | |
| CSymmDataOptions | |
| CSymmDataOptionsCreator | |
| 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 | |
| ►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 |
| 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 | |
| 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 |
| ►Npose_stream | |
| CExtendedPoseInputStream | |
| CLazySilentFilePoseInputStream | |
| CMetaPoseInputStream | |
| CPDBPoseInputStream | |
| CPoseInputStream | |
| CSilentFilePoseInputStream | |
| 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! |
| CImportPoseOptionsCreator | |
| CPDBSilentStruct | |
| CPDBSilentStructCreator | Creator for the PDBSilentStruct class |
| CPoseFromPDBLoader | |
| CPoseFromPDBLoaderCreator | |
| ►Nindexed_structure_store | |
| CBinaryFragmentStoreBackend | |
| CFragmentLookup | |
| CFragmentLookupResult | |
| CFragmentSpecification | |
| CFragmentStore | |
| CSSHashedFragmentStore | |
| CStructureStoreManager | |
| ►Ninit | |
| Cpre_talaris_2013_behavior_settings | |
| ►Nio | |
| ►Nexternal | |
| CPsiPredInterface | |
| CPsiPredResult | |
| ►Npdb | |
| CField | |
| CRecordCollection | |
| ►Npose_from_sfr | |
| CGeometricRenameIsomorphismCallback | |
| CGeometricRenameVerticiesEquivalent | Will consider two verticies equivalent if they have the same element |
| 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 |
| CSilentFileLoader | |
| CSilentFileLoaderCreator | Creator for the SilentFileLoader class |
| CSilentFileOptions | |
| CSilentFileRMOptions | |
| CSilentFileRMOptionsCreator | Creator for the SilentFileRMOptions class |
| 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 header 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 | |
| ►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 | |
| CFixbbSimAnnealer | |
| CMultiCoolAnnealer | |
| CRotamerAssigningAnnealer | |
| CRotSub | |
| CSimAnnealerBase | |
| ►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 | |
| 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 | |
| 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 | |
| ►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 | |
| 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 | |
| ►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_ |
| CSymmetricRotamerSetFactory | |
| 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 | |
| CRotamerSetsBase | |
| 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 | |
| CRotamericSingleResiduePeptoidLibrary | |
| 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 | |
| CSingleResiduePeptoidLibrary | |
| CSingleResiduePeptoidLibraryCreator | |
| 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 | |
| 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 | |
| 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 | |
| CIncludeCurrent | |
| CIncludeCurrentCreator | |
| CIncludeCurrentRLT | |
| CIncludeCurrentRLTCreator | |
| CInitializeExtraRotsFromCommandline | |
| CInitializeExtraRotsFromCommandlineCreator | |
| CInitializeFromCommandline | |
| CInitializeFromCommandlineCreator | |
| CInitializeFromOptionCollection | Retrieves an OptionCollection from the DataMap |
| CInitializeFromOptionCollectionCreator | |
| 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 | |
| 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 | |
| CRestrictAbsentCanonicalAASCreator | |
| CRestrictAbsentCanonicalAASRLT | |
| CRestrictAbsentCanonicalAASRLTCreator | |
| CRestrictResidueToRepacking | RestrictResidueToRepacking |
| CRestrictResidueToRepackingCreator | |
| CRestrictToRepacking | |
| CRestrictToRepackingCreator | |
| CRestrictToRepackingRLT | |
| CRestrictToRepackingRLTCreator | |
| 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 | |
| CClashBasedRepackShellSelector | |
| CClashBasedRepackShellSelectorCreator | |
| ►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 deprecated, it calls APOLAR to allow nonpolar residues and packing |
| CAPOLAR | APOLAR allows nonpolar residues and packing |
| CAUTO | AUTO suggests that a packer can/should reconsider the design setting at a/each residue |
| CEMPTY | EMPTY disallows all canonical and noncanonical residues |
| 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 |
| CNC | NC handles explicit allowance of noncanonical residue types |
| 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 and packing |
| CPIKNA | PIKNA allows nucleic acid residues specifed in a following string |
| CPIKRNA | PIKRNA allows nucleic acid residues specifed in a following string |
| CPOLAR | POLAR allows polar residues and packing |
| CRESET | RESET restores the list of allowd residue types to the CAAs |
| 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 | |
| ►Npose | |
| ►Ncarbohydrates | |
| CGlycanTreeSetObserver | The CacheablePoseObserver version of GlycanTreeSet that will react to pose length changes. |
| ►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 | |
| CAtom_Bin | |
| CBasePair | |
| CBaseStack | |
| Cprincipal_angle_degrees | |
| CRNA_IdealCoord | |
| 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 |
| 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 |
| 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 |
| CResidueIndexDescriptionFromFile | ResidueIndexDescriptionFromFile differs from its parent only in its error reporting when a residue index resolution fails: it prints the file name and the line number that the residue index data came from |
| 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 | |
| ►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 | Mover creator for the AmbiguousConstraint constraint |
| CAmbiguousNMRConstraint | |
| CAmbiguousNMRConstraintCreator | Mover creator for the AmbiguousNMRConstraint constraint |
| CAmbiguousNMRDistanceConstraint | |
| CAmbiguousNMRDistanceConstraintCreator | Mover creator for the AmbiguousNMRDistanceConstraint constraint |
| CAngleConstraint | An Angular Constraint |
| CAngleConstraintCreator | Mover creator for the AngleConstraint constraint |
| CAtomPairConstraint | |
| CAtomPairConstraintCreator | Mover 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 | Mover creator for the BasePairConstraint constraint |
| CBigBinConstraint | Constraint on dihedral angle formed by 4 points |
| CBigBinConstraintCreator | Mover 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 | Mover creator for the CoordinateConstraint constraint |
| CCstEnergyContainer | |
| CCstMinimizationData | |
| CCstResNeighbConstIterator | |
| CCstResNeighbIterator | |
| CDihedralConstraint | Constraint on dihedral angle formed by 4 points |
| CDihedralConstraintCreator | Mover 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 | Mover creator for the FabConstraint constraint |
| CKofNConstraint | |
| CKofNConstraintCreator | Mover creator for the KofNConstraint constraint |
| CLocalCoordinateConstraint | |
| CLocalCoordinateConstraintCreator | Mover creator for the LocalCoordinateConstraint constraint |
| CMultiConstraint | |
| CMultiConstraintCreator | Mover creator for the MultiConstraint constraint |
| CNamedAngleConstraint | |
| CNamedAngleConstraintCreator | Constraint creator for the NamedAngleConstraint |
| CNamedAtomPairConstraint | |
| 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 |
| CSequenceProfileConstraint | |
| CSequenceProfileConstraintCreator | Constraint creator for the SequenceProfileConstraint constraint |
| CSiteConstraint | |
| CSiteConstraintCreator | Mover creator for the SiteConstraint constraint |
| CSiteConstraintResidues | |
| CSiteConstraintResiduesCreator | Mover creator for the SiteConstraintResidues constraint |
| ►Ncryst | |
| CPhenixInterface | |
| CXtalMLEnergy | |
| CXtalMLEnergyCreator | |
| ►Ncustom_pair_distance | |
| CAtomPairFuncList | |
| Catoms_and_func_struct | |
| CDistanceFunc | |
| CFullatomCustomPairDistanceEnergy | |
| CFullatomCustomPairDistanceEnergyCreator | |
| 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 | |
| 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 | |
| CElectronDensityLoader | |
| CElectronDensityLoaderCreator | Creator for the ElectronDensityLoader class |
| CElectronDensityOptions | |
| CElectronDensityOptionsCreator | Creator for the ElectronDensityOptions class |
| CFastDensEnergy | |
| CFastDensEnergyCreator | |
| CKromerMann | |
| COneGaussianScattering | |
| CposeCoord | |
| ►Nelectron_density_atomwise | |
| CElecDensAtomwiseEnergy | |
| CElecDensAtomwiseEnergyCreator | |
| CElectronDensityAtomwise | |
| CPoseSequence | |
| ►Netable | |
| ►Ncoulomb | |
| CCoulomb | |
| ►Ncount_pair | |
| CCountPair1B | |
| CCountPair2B | |
| CCountPairAll | |
| CCountPairCrossover3 | |
| CCountPairCrossover34 | |
| 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 | |
| CCubicPolynomial | |
| 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 | |
| CSplineParameters | SplineParameters is a simple struct for holding the cubic spline polynomials used in the etable to interpolate the lennard-jones attractive and LK-solvation terms to zero smoothly. These splines have exactly two knots to represent them, and the same x values are used for all the knots: thus the only parameters needed are the y values at the knots, and the second-derivatives for the polynomials at knots |
| 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 | |
| CFiberDiffractionLoader | |
| CFiberDiffractionLoaderCreator | |
| CFiberDiffractionOptions | |
| CFiberDiffractionOptionsCreator | Creator for the FiberDiffractionOptions class |
| 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 | |
| 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 | |
| ►Nhbtrie | |
| CHBAtom | |
| CHBCountPairFunction | |
| CHBCPData | |
| CFadeInterval | Classic FadeInterval |
| 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 | |
| CPolynomial_1d | |
| CSSWeightParameters | |
| ►Ninterface_ | |
| CDDPlookup | |
| CDDPscore | |
| CDDPscoreCreator | |
| ►Nlkball | |
| ►Nlkbtrie | |
| CLKBAtom | |
| CLKBTrieEvaluator | |
| CLK_BallEnergy | |
| CLK_BallEnergyCreator | |
| CLKB_ResidueInfo | |
| CLKB_ResiduesInfo | |
| CLKB_ResPairMinData | |
| CScoredBridgingWater | |
| CWaterBuilder | |
| ►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 |
| CMPLipoEnergy | Membrane Lipophilicity term |
| CMPLipoEnergyCreator | Creator Class for MPLipoEnergy |
| 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 |
| 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 | |
| CAspartimidePenaltyEnergy | |
| CAspartimidePenaltyEnergyCreator | |
| CBBDepCartBondedParameters | |
| CBBIndepCartBondedParameters | |
| 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 | |
| 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 | |
| CGoapEnergy | |
| CGoapEnergyCreator | |
| CGoapRsdType | |
| CHybridVDW_Energy | |
| CHybridVDW_EnergyCreator | |
| CHydroxylTorsionEnergy | |
| CHydroxylTorsionEnergyCreator | |
| CIdealParametersDatabase | |
| CIntermolEnergy | |
| CIntermolEnergyCreator | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| ►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 | |
| CXfrag | |
| CXfragSet | |
| CXfres | |
| ►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_DataInfo | Keep track of RNA chemical mapping data inside the pose |
| CRNA_Datum | |
| CRNA_DMS_LowResolutionPotential | |
| CRNA_DMS_Potential | |
| CRNA_Reactivity | |
| 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_FilteredBaseBaseInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| 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_PairwiseLowResolutionEnergy | |
| CRNA_PairwiseLowResolutionEnergyCreator | |
| 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_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_LowResPotential | |
| CRNP_LowResStackData | |
| CRNP_LowResStackEnergy | |
| CRNP_LowResStackEnergyCreator | |
| CStackElecEnergy | |
| CStackElecEnergyCreator | |
| ►Nsasa | |
| CLeGrandSasa | LeGrand SASA approximation method Used by SasaCalc but can be used by itself |
| CSasaCalc | Main interface to sasa calculations outside of pose metrics |
| CSasaMethod | Abstract base class for SasaMethods. Feel free to edit as needed |
| ►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: |
| CMolecularSurfaceCalculator | |
| CShapeComplementarityCalculator | |
| CShapeComplementarityCalculatorException | |
| ►Nsolid_surface | |
| CSurfaceEnergies | |
| ►Nsym_e | |
| CsymECreator | |
| CsymEnergy | |
| ►Nsymmetry | |
| CSymmetricEnergies | |
| CSymmetricScoreFunction | |
| ►Ntrie | |
| CCPDataCorrespondence | |
| CRotamerDescriptor | |
| CRotamerDescriptorAtom | |
| CRotamerTrie | |
| CRotamerTrieBase | |
| CTrieCollection | |
| CTrieCountPairBase | |
| CTrieNode | |
| ►Nvdwaals | |
| CVDW_Energy | |
| CVDW_EnergyCreator | |
| CVDWAtom | |
| CVDWTrieCountPair1B | |
| CVDWTrieEvaluator | |
| ►CAPBSConfig | |
| CI_PARAM | |
| CR_PARAM | |
| CAPBSResult | |
| CAPBSWrapper | |
| CAtomNeighbor | Atom-atom neighborlist object |
| CAtomVDW | |
| CBB_Pos | |
| 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 | |
| CGenBornPoseInfo | |
| CGenBornPotential | |
| CGenBornResidueInfo | |
| CGenBornRotamerSetInfo | |
| 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_ss | |
| CPairEPotential | |
| CPDatom | |
| CPDinter | |
| CPDvertex | |
| 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 | |
| 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 | |
| CSS_Info | |
| CSS_Killhairpins_Info | |
| CStrands | |
| CTenANeighborEdge | |
| CTenANeighborGraph | |
| CTenANeighborNode | |
| CTMscore | |
| CTMscoreStore | |
| CTorsionParams | |
| CTwelveANeighborEdge | |
| CTwelveANeighborGraph | |
| CTwelveANeighborNode | |
| CUnfoldedStatePotential | |
| CVdWTinkerPoseInfo | |
| CVdWTinkerPotential | |
| CVdWTinkerResidueInfo | |
| CVdWTinkerRotamerSetInfo | |
| CWaterAdductHBondPotential | |
| ►Nselect | |
| ►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 | |
| CBinSelector | A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin) |
| CBinSelectorCreator | |
| CCachedResidueSubset | |
| CChainSelector | |
| CChainSelectorCreator | |
| CCloseContactResidueSelector | A class that finds the neighboring residues for a particular residue by looking at atom-atom distances |
| CCloseContactResidueSelectorCreator | |
| 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 | |
| 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). Detection and mapping from PDB to Rosetta residue numbers is done internally |
| CResidueIndexSelectorCreator | |
| 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 | |
| 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 |
| 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 | |
| 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 |
| CSymmetricalResidueSelectorCreator | |
| CTrueResidueSelector | |
| CTrueResidueSelectorCreator | |
| ►Nutil | |
| CSelectResiduesByLayer | |
| ►Nsequence | |
| CABEGO | Abego elments |
| CABEGOManager | Manager for abego |
| CAligner | |
| CAlignerFactory | |
| CAnnotatedSequence | |
| CCell | |
| 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 | |
| ►Nutil | |
| CChainbreakUtil | |
| CSVNVersion | |
| ►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 | |
| 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 | |
| CKinematicTaskControl | |
| CLoopJumpFoldCst | |
| CMembraneAbinitio | |
| COrderSortPredicate | |
| CPairingStatEntry | |
| CPairingStatistics | |
| CPcaEvaluator | |
| CProtocol | |
| CResolutionSwitcher | |
| CShowViolation | |
| CStage1Sampler | |
| CStrandConstraints | |
| CStructureStore | |
| CTemplate | |
| CTemplateJumpSetup | |
| CTemplates | |
| ►Nanalysis | |
| CInterfaceAnalyzerMover | Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method |
| CInterfaceAnalyzerMoverCreator | |
| CInterfaceData | All interface data. Unless otherwise specified, they refer specifically to the interface |
| CLoopAnalyzerMover | |
| CLoopAnalyzerMoverCreator | |
| CPackStatMover | |
| CPeptideDeriverBasicStreamOutputter | Outputs a Peptiderive report to a stream in a basic, easily parsable format |
| CPeptideDeriverFilter | Implementation of the Peptiderive protocol - given a pose, it evaluates the binding energy of linear stretches, of given lengths, and indicates which of these contributes more than others to the interaction energy. It also reports on and optionally models cyclizable peptides |
| CPeptideDeriverFilterCreator | |
| CPeptideDeriverMarkdownStreamOutputter | Outputs a Markdown formatted Peptiderive report to a stream |
| CPeptideDeriverOutputter | Abstract base class for handling calculation outputs from PeptideDeriverFilter Since PeptideDeriverFilter might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. This is an attempt to decouple the calculation from the representation of results. Representation of results is delegated to implementors of this class |
| CPeptideDeriverOutputterContainer | Container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those |
| CPeptideDeriverPoseOutputter | Outputs poses at different points of the Peptiderive protocol, according to the given set of options |
| CPerResidueInterfaceData | All per residue interface data and residue averages. Interface Residues only |
| ►Nanchored_design | |
| CAnchor | Anchor class provides for the "anchor" part of a scaffold in anchored interface design |
| CAnchoredDesignMover | |
| CAnchoredPerturbMover | |
| CAnchoredRefineMover | |
| CAnchorMoversData | This data class wraps all the data needed for the AnchoredDesign movers |
| ►Nantibody | |
| ►Nclusters | |
| CBasicCDRClusterSet | Basic container class for CDRClusterSet, with some extra information |
| CCDRCluster | Simple class to hold and access CDRCluster info for a region of the pose |
| CCDRClusterEnumManager | Interface to this class is in AntibodyInfo. Should be a singleton |
| CCDRClusterFeatures | |
| CCDRClusterFeaturesCreator | |
| CCDRClusterMatcher | Simple class for identifying CDR clusters of an antibody or protein structure |
| CCDRClusterSet | Class that can determine a CDR Cluster, hold that information, and give it out when asked |
| CClusterData | Holds data for each cluster type |
| ►Nconstraints | |
| CCDRDihedralConstraintMover | Add Cluster or General Dihedral CircularHarmonic constraints to a CDR. Cluster constraints currently only work for AHO renumbered CDRs. (This will be rafactored to create constraints on-the-fly from cluster Mean/SD instead of from cst files.) |
| CCDRDihedralConstraintMoverCreator | |
| CParatopeEpitopeSiteConstraintMover | Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope. Will only add the constraint if not already present |
| CParatopeEpitopeSiteConstraintMoverCreator | |
| CParatopeSiteConstraintMover | Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead |
| CParatopeSiteConstraintMoverCreator | |
| ►Ndesign | |
| CAntibodyDesignEnumManager | |
| CAntibodyDesignMover | This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase. Up-to-date versions can be downloaded from |
| CAntibodyDesignMoverCreator | |
| CAntibodyDesignProtocol | Main AntibodyDesignProtocol, tieing together individual movers and classes. Main mover for application |
| CAntibodyDesignProtocolCreator | |
| CAntibodySeqDesignTFCreator | Create a TaskFactory or individual TaskOperations based on a set of options These options are mainly for per-CDR and per-framework control of sequence design |
| CCDRGraftDesignOptions | Class that holds CDRGraftDesign Options. Now that GraftDesign is not a separate 'thing', this should be split into CDRGraftOptions and CDRMinOptions eventually |
| CCDRGraftDesignOptionsParser | |
| CCDRSeqDesignOptions | |
| CCDRSeqDesignOptionsParser | |
| CGeneralAntibodyModeler | Basic Class that can run modeling for various protocols. Does not do any design. Setup design TF via AntibodySeqDesignTFCreator |
| CMutantPosition | |
| CMutateFrameworkForCluster | Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations |
| CMutateFrameworkForClusterCreator | |
| CNativeAntibodySeq | Class that keeps track of the 'native' sequence during design. Native means that no design has occured. Used for conservative base design to keep it from hopping around residue types |
| CPDBNumbering | Super-basic numbering struct |
| ►Ngrafting | |
| C_AE_cdr_detection_failed_ | |
| C_AE_cdr_undefined_ | |
| C_AE_grafting_failed_ | |
| C_AE_invalid_cdr_region_ | |
| C_AE_numbering_failed_ | |
| C_AE_scs_failed_ | |
| C_AE_unexpected_region_length_ | |
| CGrafting_Base_Exception | |
| ►Nresidue_selector | |
| CAntibodyRegionSelector | A simple selector to select residues of particular antibody regions |
| CAntibodyRegionSelectorCreator | |
| CCDRResidueSelector | Select CDR residues |
| CCDRResidueSelectorCreator | |
| ►Nsnugdock | |
| CSnugDock | MoveSet step of Snugdock as described in: |
| CSnugDockCreator | |
| CSnugDockProtocol | |
| ►Ntask_operations | |
| CAddCDRProfileSetsOperation | Add Cluster-based sets of mutations as a TaskOperation. Essentially samples full sequences of CDRs within a particular CDR cluster randomly each time the packer is called. Does this for each CDR |
| CAddCDRProfileSetsOperationCreator | |
| CAddCDRProfilesOperation | Add Cluster-based CDR Profiles as the task operation for the set of CDRs by default. See protocols/toolbox/task_operations/ResidueProbTaskOperation for more |
| CAddCDRProfilesOperationCreator | |
| CDisableAntibodyRegionOperation | A TaskOperation that Disables packing +/or design of a particular antibody region. By Default, disables packing and design of the cdr_region. Make sure to set the region you want disabled |
| CDisableAntibodyRegionOperationCreator | |
| CDisableCDRsOperation | TaskOperation to Disable Packing and/or design of a set of CDRs. By default, disables both Packing and Design of all CDRs |
| CDisableCDRsOperationCreator | |
| CRestrictToCDRsAndNeighbors | Task Operation to restrict packing/design to specific CDRs and neighbors. See DisableAntibodyRegionOperation and DisableCDRsOperation further restrict TaskFactory |
| CRestrictToCDRsAndNeighborsCreator | |
| CAb_TemplateInfo | Specifically for AntibodyModeling protocol templates. Not for general use |
| CAntibodyCDRGrafter | Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody. Independant of antibody and CDR modeling. Results in 100 percent loop closure if using both graft algorithms |
| CAntibodyCDRGrafterCreator | |
| CAntibodyDatabaseManager | Class responsible for loading information from the AntibodyDatabase |
| CAntibodyEnumManager | Interface to this class is in AntibodyInfo |
| CAntibodyFeatures | Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics |
| CAntibodyFeaturesCreator | Creator for the HBondParameterFeatures class |
| CAntibodyInfo | This class is used to get all relevant information you would need when dealing with an antibody |
| CAntibodyModelerProtocol | |
| CAntibodyNumbering | |
| CAntibodyNumberingConverterMover | Converts numbering schemes of an antibody, independant of AntibodyInfo. By default, works on a SINGLE antibody FAB with chains L and H, as in the rest of Rosetta |
| CAntibodyNumberingConverterMoverCreator | |
| CAntibodyNumberingParser | Class responsible for reading database Numbering Scheme definitions and their transforms from the database |
| CCDRDBPose | |
| CCDRDBSequence | |
| CCDRSetOptions | Class that holds instructions for a single CDR for loading from the antibody database. Default is instructions to load all CDRs from the database |
| CCDRSetOptionsParser | Parses CDRSetOptions for a single CDR at a time from a simple instruction file |
| CCDRsMinPackMin | |
| CCloseOneCDRLoop | Closes only one CDR onto a framework |
| CFrameWork | |
| CGraftCDRLoopsProtocol | |
| CGraftedStemOptimizer | Grafts only one CDR onto a framework |
| CGraftOneCDRLoop | Grafts only one CDR onto a framework |
| CH3CterInsert | H3 CDR, Fragment Insertion and CCD |
| CH3PerturbCCD | |
| CH3RefineCCD | |
| CLHRepulsiveRamp | |
| CLHRepulsiveRampLegacy | |
| CLHSnugFitLegacy | |
| CModelCDRH3 | Ab initio modeling of CDR H3 loop |
| CParatopeMetric | Convenience struct for passing around paratope data, including individual data for cdrs. CDRs not present default to 0. Templates are used mainly to have Size/ Real or string values |
| CPDBLandmark | Class that was once a struct; Used for matching pdb information between numbering schemes and cdr definitions |
| CRefineBetaBarrel | |
| CRefineOneCDRLoop | |
| CRefineOneCDRLoopCentroid | |
| ►Nantibody_legacy | |
| CAntibody | Antibody definition |
| CAntibodyModeler | |
| CCDRH3Modeler | Ab initio modeling of CDR H3 loop |
| CCloseOneMover | Closes only one CDR onto a framework |
| CGraftMover | Grafts a series of CDR onto a framework |
| CGraftOneMover | Grafts only one CDR onto a framework |
| CLoopRlxMover | Closes only one CDR onto a framework |
| ►Nbackbone_moves | |
| ►Nlocal_backbone_mover | |
| ►Nfree_peptide_movers | |
| CCircularPermuteFreePeptideMover | Circularly permute the torsions on the free peptide |
| CFreePeptideMover | Base class for free peptide movers |
| CLongAxisRotationFreePeptideMover | Rotate the free peptide along the axis formed by its first and last CA atom |
| CShearFreePeptideMover | Change the psi torsion of a residue and phi torsion of its subsequent residue by a opposite value |
| CTranslationFreePeptideMover | Translate the free peptide by a cartesian vector |
| ►Ngap_solution_pickers | |
| CGapSolutionPicker | Base class for picking solution for a gap |
| CRandomGapSolutionPicker | Pick a solution randomly |
| CFreePeptide | FreePeptide represents a free peptide |
| CGapCloser | GapCloser closes the gaps after moving the free peptide |
| CLocalBackboneMover | LocalBackboneMover moves a stretch of backbone locally |
| CLocalBackboneMoverCreator | |
| CResidue | Residue is a helper class for FreePeptide |
| ►Nbackrub | |
| CBackrubMover | Class for applying backrub moves to arbitrary protein segments |
| CBackrubMoverCreator | |
| CBackrubProtocol | |
| CBackrubProtocolCreator | |
| CBackrubSegment | Class for holind information about individual backrub segments |
| CBackrubSidechainMover | |
| CBackrubSidechainMoverCreator | |
| ►Nboinc | |
| CBoinc | |
| CBoincCurrentPoseObserver | |
| CBoincSharedMemory | |
| ►Nbranch_angle | |
| CBranchAngleOptimizer | |
| CBranchCoef1 | Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors |
| CBranchCoef2 | Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors |
| CBranchParam1 | Class to store bond angle energy parameters around a single atom atom with three bonded neighbors |
| CBranchParam2 | Class to store bond angle energy parameters around a single atom atom with four bonded neighbors |
| ►Ncanonical_sampling | Algorithms for rigorously sampling native state ensembles. See disclaimer in detailed description |
| ►Nmc_convergence_checks | |
| CDataBuffer | |
| CEXCN_Heat_Converged | |
| CEXCN_Pool_Converged | |
| CHeat_ConvergenceCheck | |
| CHierarchicalLevel | |
| CHPool_RMSD | |
| CPool_ConvergenceCheck | |
| CPool_Evaluator | |
| CPool_RMSD | |
| CPoolData | |
| ►CAsyncMPITemperingBase | |
| CExchangeRequest | |
| CBiasedMonteCarlo | |
| ►CBiasEnergy | |
| CHistogram | |
| CCanonicalSamplingMover | |
| ►CDbTrajectoryRecorder | Record a trajectory to an SQL database |
| CFrame | Helper struct used store cached poses |
| CDbTrajectoryRecorderCreator | RosettaScripts factory for DbTrajectoryRecorder |
| CFixedTemperatureController | Maintain a constant temperature |
| CHamiltonianExchange | |
| CHamiltonianExchangeCreator | RosettaScripts factory for HamiltonianExchange |
| CMetricRecorder | Periodically output miscellaneous information |
| CMetricRecorderCreator | RosettaScripts factory for MetricRecorder |
| CMetropolisHastingsMover | Manage the main loop of a canonical Monte Carlo simulation |
| CMetropolisHastingsMoverCreator | RosettaScripts factory for MetropolisHastingsMover |
| CMultiTemperatureTrialCounter | Keep track of trial statistics for any number of replicas |
| CParallelTempering | |
| CParallelTemperingCreator | RosettaScripts factory for ParallelTempering |
| CPatchOperation | |
| CPDBTrajectoryRecorder | Record a trajectory to the PDB file format |
| CPDBTrajectoryRecorderCreator | RosettaScripts factory for PDBTrajectoryRecorder |
| CProgressBarObserver | Print an progress bar that updated on each iteration |
| CProgressBarObserverCreator | RosettaScripts factory for ProgressBarObserver |
| CSidechainMetropolisHastingsMover | Run a sidechain-only canonical Monte Carlo simulation |
| CSidechainMetropolisHastingsMoverCreator | RosettaScripts factory for SidechainMetropolisHastingsMover |
| CSilentTrajectoryRecorder | Record a trajectory to the rosetta-specific silent file format |
| CSilentTrajectoryRecorderCreator | RosettaScripts factory for SilentTrajectoryRecorder |
| CSimulatedTempering | |
| CSimulatedTemperingCreator | RosettaScripts factory for SimulatedTempering |
| CTemperatureController | Base class for controlling the temperature of a simulation |
| CTemperingBase | Base class for tempering Monte Carlo optimizations |
| CThermodynamicMover | Base class for moves that can obey detailed balance |
| CThermodynamicObserver | Base class for reporting and recording data from a simulation |
| CTrajectoryRecorder | Base class for recording a simulation trajectory |
| CTrialCounterObserver | Record the acceptance rate for every type of move attempted |
| CTrialCounterObserverCreator | RosettaScripts factory for TrialCounterObserver |
| CWTEBiasEnergy | |
| ►Ncarbohydrates | |
| CGlycanRelaxMover | Main mover for Glycan Relax, which optimizes glycans in a pose. Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. Currently uses a random sampler with a set of weights to each mover for sampling |
| CGlycanRelaxMoverCreator | |
| CGlycanTreeMinMover | A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector |
| CGlycanTreeMinMoverCreator | |
| CLinkageConformerMover | This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues |
| CLinkageConformerMoverCreator | |
| CSimpleGlycosylateMover | A mover for glycosylation of biological glycosylations. Currently glysolylation is done based on string, not from PDB. Use GlycanRelax to model the resulting glycosylation! |
| CSimpleGlycosylateMoverCreator | |
| ►Ncartesian | |
| CCartesianAtom | |
| CMD_Angle | |
| CMD_Bond | |
| CMD_HarmonicDihedral | |
| CMolecularDynamics | |
| ►Ncheckpoint | |
| CCheckPointer | |
| CFileBuffer | |
| CTimer | : singleton checkpoint timer class |
| ►Ncluster | |
| CAPCluster | Public interface for doing affinity propagation clustering |
| CAssignToClustersMover | |
| CCluster | |
| CClusterBase | |
| CClusterPhilStyle | |
| CClusterPhilStyle_Loop | |
| CClusterPhilStyle_PoseReporter | |
| CDataPoint | Data structure for one input data point for affinity propagation clustering |
| CEnsembleConstraints | |
| CEnsembleConstraints_Simple | |
| CExemplar | Data structure for one similarity measurement (s_ik) for affinity propagation clustering |
| CGatherPosesMover | |
| ►Ncoarse_rna | |
| CCoarseRNA_Fragments | |
| CCoarseRNA_LoopCloser | The RNA de novo structure modeling protocol |
| CSourcePositions | |
| ►Ncomparative_modeling | |
| ►Nfeatures | |
| CResidueFeature | |
| CResidueFeatureFactory | |
| CSSFeature | |
| CTorsionFeature | |
| CAlign_RmsdEvaluator | |
| CAlign_RotamerEvaluator | |
| CAlignmentCluster | |
| CAlignmentClustering | |
| CAlignmentSet | |
| CAlignRmsdTargetEvaluatorCreator | Creator for the AlignRmsdTargetEvaluatorCreator class |
| CExtraThreadingMover | |
| CGenericJobInputter | |
| CGenericJobInputterCreator | |
| CIgnoreSubsetConstraintSet | |
| CLoopRelaxMover | |
| CLoopRelaxMoverCreator | |
| CLoopRelaxThreadingMover | |
| CMultiThreadingMover | |
| CPartialThreadingMover | |
| CRecoverSideChainsMover | |
| CStealLigandMover | |
| CStealSideChainsMover | |
| CThreadingJob | |
| CThreadingJobInputter | |
| CThreadingJobInputterCreator | |
| CThreadingMover | |
| ►Nconstraint_generator | |
| CAddConstraints | Adds constraints generated by ConstraintGenerators to a pose |
| CAddConstraintsCreator | |
| ►CAtomPairConstraintGenerator | Generates atom pair constraints for a set of residues from the current or reference pose |
| CMappedAtom | |
| CAtomPairConstraintGeneratorCreator | |
| CConstraintGenerator | Pure virtual base class |
| CConstraintGeneratorCreator | |
| CConstraintGeneratorFactory | |
| CConstraintGeneratorRegistrator | This templated class will register an instance of an ConstraintGeneratorCreator (class T) with the ConstraintGeneratorFactory. It will ensure that no ConstraintGenerator creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CConstraintsManager | Manages lists of constraints generated by ConstraintGenerators |
| CConstraintsMap | Cacheable data map to cache constraint pointers in the pose |
| CCoordinateConstraintGenerator | Generates coodinate constraints |
| CCoordinateConstraintGeneratorCreator | |
| CDistanceConstraintGenerator | Generates AtomPair constraints to enforce a given distance between two residue subsets |
| CDistanceConstraintGeneratorCreator | |
| CEXCN_RemoveCstsFailed | |
| CHydrogenBondConstraintGenerator | This constraint generator generates constraints for favoring formation of hydrogen bonds |
| CHydrogenBondConstraintGeneratorCreator | |
| CHydrogenBondInfo | Database to lookup atoms for hydrogen bonding |
| CHydrogenBondingAtom | |
| CRemoveConstraints | Removes constraints generated by a ConstraintGenerator |
| CRemoveConstraintsCreator | |
| CTerminiConstraintGenerator | Generates distance constraints between the upper and lower termini |
| CTerminiConstraintGeneratorCreator | |
| ►Nconstraints_additional | |
| CAmbiguousMultiConstraint | |
| CBindingSiteConstraint | |
| CBindingSiteConstraintCreator | Mover creator for the BindingSiteConstraint constraint |
| CCombinedConstraintEvaluator | |
| CCombinedConstraintEvaluatorCreator | Creator for the CombinedConstraintsEvaluatorCreator class |
| CCOMCoordinateConstraint | |
| CConstraintEvaluator | |
| CConstraintEvaluatorCreator | Creator for the ConstraintsEvaluatorCreator class |
| CMaxSeqSepConstraintSet | |
| CNamedAtomPairConstraintCreator | This class can be used to replace the standard AtomPairConstraintsCreator; see BrokerMain.cc for an example |
| CSequenceCoupling1BDConstraint | |
| CSequenceCoupling1BDConstraintCreator | Mover creator for the SequenceCoupling1BDconstraint |
| CSequenceCouplingConstraint | |
| CSequenceCouplingConstraintCreator | Mover creator for the SequenceCouplingconstraint |
| ►Ncontact_map | |
| CContact | Simple class representing a contact between two atoms |
| CContactMap | |
| CContactMapCreator | |
| CContactPartner | Simple class that holds the information on an atom involved in a contact |
| ►Ncoupled_moves | |
| CCoupledMovesProtocol | |
| ►Ncryst | |
| CCheshireCell | A struct used by spacegroup.cc and its helper functions |
| CDockLatticeMover | |
| CDockLatticeMoverCreator | |
| CFitBfactorsMover | |
| CFitBfactorsMoverCreator | |
| CLoadDensityMapMover | |
| CLoadDensityMapMoverCreator | |
| CMakeLatticeMover | |
| CMakeLatticeMoverCreator | |
| CMakeLayerMover | |
| CMakeLayerMoverCreator | |
| CRecomputeDensityMapMover | |
| CRecomputeDensityMapMoverCreator | |
| CReportGradientsMover | |
| CReportGradientsMoverCreator | |
| CSetCrystWeightMover | |
| CSetCrystWeightMoverCreator | |
| CSetRefinementOptionsMover | |
| CSetRefinementOptionsMoverCreator | |
| CSpacegroup | |
| CTagPoseWithRefinementStatsMover | |
| CTagPoseWithRefinementStatsMoverCreator | |
| CUpdateCrystInfo | |
| CUpdateCrystInfoCreator | |
| CUpdateSolventMover | |
| CUpdateSolventMoverCreator | |
| CWallpaperGroup | |
| ►Ncyclic_peptide | |
| ►Nthreefold_linker | |
| CTBMB_Helper | A derived class of the ThreefoldLinkerMoverHelper base class, used to set up the 1,3,5-tris(bromomethyl)benzene (TBMB) cross-linker |
| CThreefoldLinkerMoverHelper | A base class for helper objects that the ThreefoldLinkerMover uses to set up specific types of threefold linkers |
| CCreateAngleConstraint | |
| CCreateAngleConstraintCreator | |
| CCreateDistanceConstraint | |
| CCreateDistanceConstraintCreator | |
| CCreateTorsionConstraint | |
| CCreateTorsionConstraintCreator | |
| CCycpepSymmetryFilter | A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry |
| CCycpepSymmetryFilterCreator | |
| CDeclareBond | |
| CDeclareBondCreator | |
| CFlipChiralityMover | |
| CFlipChiralityMoverCreator | |
| COversaturatedHbondAcceptorFilter | This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds |
| COversaturatedHbondAcceptorFilterCreator | |
| CPeptideCyclizeMover | |
| CPeptideCyclizeMoverCreator | |
| CPeptideStubMover | |
| CPeptideStubMoverCreator | |
| CSymmetricCycpepAlign | Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover |
| CSymmetricCycpepAlignCreator | |
| CThreefoldLinkerMover | This mover links three cysteine residues with a threefld-symmetric cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), andthen optionally relaxes the whole structure |
| CThreefoldLinkerMoverCreator | |
| CTryDisulfPermutations | |
| CTryDisulfPermutationsCreator | |
| ►Ncyclic_peptide_predict | |
| CSimpleCycpepPredictApplication | Application-level code for simple_cycpep_predict application |
| CSimpleCycpepPredictApplication_MPI_JobResultsSummary | A class for summarizing the result of an MPI-mode job run with the SimpleCycpepPredictApplication |
| ►Nddg | |
| CddGMover | |
| ►NddG | |
| CddGData | |
| ►Ndenovo_design | |
| ►Narchitects | |
| CBetaSheetArchitect | Architect that creates a beta sheet |
| CBetaSheetArchitectCreator | |
| CBlueprintArchitect | Designs a structure using a Blueprint file |
| CBlueprintArchitectCreator | |
| CCompoundArchitect | Architect that creates a StructureData using multiple architects |
| CCompoundArchitectCreator | |
| CDeNovoArchitect | For planning ideal pieces of structures |
| CDeNovoArchitectCreator | |
| CDeNovoArchitectFactory | Creates DeNovo architects |
| CDeNovoMotifArchitect | For planning arbitrary motifs |
| CEXCN_PreFilterFailed | |
| CHelixArchitect | Architect for helices |
| CHelixArchitectCreator | |
| CPoseArchitect | Design segments based on a pose |
| CPoseArchitectCreator | |
| CSecStructInfo | |
| CStrandArchitect | Architect that creates a beta strand |
| CStrandArchitectCreator | |
| CStructureArchitect | Designs topologies |
| ►Ncomponents | |
| CAlias | |
| CBondInfo | |
| CBuildPhases | |
| CCompoundPerturber | "mutates" a set of mixed architects |
| CConnectionPerturber | "mutates" a connection |
| CDivideAndConqueror | Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece |
| CEnumeratedVectorSelector | Selects items sequentially from a vector |
| CEXCN_Fold | Exception thrown by PoseFolder::apply to indicate folding was not successful |
| CEXCN_PoseInconsistent | |
| CEXCN_RemarksNotPresent | |
| CExtendedPoseBuilder | Builds a pose from StructureData |
| CFoldGraph | |
| CHelixPairing | |
| CHelixPerturber | "mutates" a helix |
| CHelixSheetPairing | |
| CIdealAbegoGenerator | Logic for selection of abego values |
| CNamedSolution | |
| CNamedSolutions | |
| CNullPerturber | Perturber that does nothing |
| CNullPoseFolder | Folds a pose using random phi/psi torsions |
| CPicker | Class used for picking/caching fragments |
| CPoseFolder | Given a pose with all residues, and a StructureData object, assign a 3D conformation to the pose |
| CRandomTorsionPoseFolder | Folds a pose using random phi/psi torsions |
| CRandomVectorSelector | Selects items from a vector randomly |
| CRemodelLoopMoverPoseFolder | Folds residues in a pose using RemodelLoopMover |
| CResidueDihedrals | |
| CSegment | Manages information about segments of residues |
| CSegmentCounts | |
| CSegmentPairing | |
| CSegmentPairSet | |
| CSheetDB | Class used to create/manipulate a database of sheets using a list of pdb files |
| CSolutionPredicate | |
| CSolutionSorter | |
| CStrandPairing | |
| CStructureData | |
| CStructureDataCreator | |
| CStructureDataFactory | Singleton for creating StructureData objects |
| CStructureDataObserver | Cacheable observer that keeps track of what length events occured |
| CStructureDataPerturber | Classes for altering StructureData objects on the fly |
| CStructureSlice | |
| CStructureSlicePredicate | |
| CVectorSelector | Selects items from a vector using different methods |
| CVLBProtected | |
| ►Nconnection | |
| CAreConnectablePredicate | |
| CConnectionArchitect | Architect for covalently joining two segments of a pose |
| CEXCN_ConnectionSetupFailed | |
| ►Nconstraints | |
| CFileConstraintGenerator | |
| CFileConstraintGeneratorCreator | |
| ►Nfilters | |
| CExposedHydrophobicsFilter | |
| CExposedHydrophobicsFilterCreator | |
| CPreProlineFilter | |
| CPreProlineFilterCreator | |
| CSSPredictionFilter | |
| CSSPredictionFilterCreator | |
| ►Nmovers | |
| CAddSegmentDataMover | Adds a segment to the structuredata |
| CAddSegmentDataMoverCreator | |
| CAlignResiduesMover | Aligns one residue onto another |
| CAlignResiduesMoverCreator | |
| CBridgeChainsCreator | |
| CBridgeChainsMover | Creates a bridge connection between two chains using remodel |
| CBridgeChainsMoverCreator | |
| CBuildDeNovoBackboneMover | Mover that builds and folds a structure via fragment insertion |
| CBuildDeNovoBackboneMoverCreator | |
| CCutAndJump | |
| CDeclareStructureDataCovalentBondMover | Declares covalent bond |
| CDeclareStructureDataCovalentBondMoverCreator | |
| CEXCN_FilterFailed | |
| CEXCN_NothingToFold | |
| CExtendChainMover | |
| CExtendChainMoverCreator | |
| CFastDesign | |
| CFastDesignCreator | |
| CFoldTreeFromFoldGraphMover | Creates and sets a new fold tree for the pose by traversing a FoldGraph |
| CFoldTreeFromFoldGraphMoverCreator | |
| CMakeAsymmetricStructureDataMover | Converts a StructureData for a symmetric pose into an asymmetric representation |
| CMakeAsymmetricStructureDataMoverCreator | |
| CRelaxScriptCommand | |
| CRotateSegmentMover | Rotates a segment in the pose |
| CRotateSegmentMoverCreator | |
| CRotationRange | |
| CSealFoldTreeMover | Creates a sealed foldtree, and removes all cutpoints from the pose |
| CSealFoldTreeMoverCreator | |
| CSetPoseSecstructFromStructureDataMover | |
| CSetResidueAliasMover | Sets a residue alias in the StructureData |
| CSetResidueAliasMoverCreator | |
| ►Nresidue_selectors | |
| CNamedSegmentSelector | Selects residues from a named segment generated by StructureArchitects |
| CNamedSegmentSelectorCreator | |
| CPairedSheetResidueSelector | Selects residues that are involved in strand-strand pairings |
| CPairedSheetResidueSelectorCreator | |
| ►Ntask_operations | |
| CAAFrequencies | |
| CAAFrequency | |
| CConsensusLoopDatabase | |
| CConsensusLoopDesignOperation | |
| CConsensusLoopDesignOperationCreator | |
| CLoopInfo | |
| CSurroundingSS | |
| CDisulfidizeMover | |
| CDisulfidizeMoverCreator | |
| ►Ndesign_opt | |
| CGreedyOptMutationMover | |
| CGreedyOptMutationMoverCreator | |
| CPointMutationCalculator | |
| ►Ndna | |
| CDesignProteinBackboneAroundDNA | |
| CDesignProteinBackboneAroundDNACreator | |
| CDNABase | |
| CDNABasepair | |
| CDNABasestep | |
| CDnaChains | |
| CDnaDesignDef | Command-line dna_defs are of the format "C.501.ADE" they are parsed here into this little class for convenience |
| CDnaInterfaceFinder | |
| CDnaInterfaceMinMover | |
| CDnaInterfaceMinMoverCreator | |
| CDnaInterfaceMultiStateDesign | Wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework |
| CDnaInterfaceMultiStateDesignCreator | |
| CDnaInterfacePacker | |
| CDnaInterfacePackerCreator | |
| CDnaNeighbor | |
| CDNAParameters | |
| CDnaPosition | |
| CPDBOutput | |
| CPositionType | Basic struct for remembering position/type information before/during/after design |
| CRestrictDesignToProteinDNAInterface | |
| CRestrictDesignToProteinDNAInterfaceCreator | |
| CResTypeSequence_lt | |
| CReversion | |
| CRotamerDNAHBondFilter | |
| CSeparateDnaFromNonDna | |
| CSeparateDnaFromNonDnaCreator | |
| CWatsonCrickRotamerCouplings | |
| CWatsonCrickRotamerCouplingsCreator | |
| ►Ndocking | |
| ►Nmembrane | |
| CMPDockingMover | Docks two proteins together in the membrane bilayer |
| CMPDockingMoverCreator | Mover Creator |
| CMPDockingSetupMover | Setup for MPDocking |
| CMPDockingSetupMoverCreator | Mover Creator |
| CMPFindInterfaceMover | |
| CMPFindInterfaceMoverCreator | Mover Creator |
| CQuickRelaxPartnersSeparately | |
| CQuickRelaxPartnersSeparatelyCreator | Mover Creator |
| ►Nstateless | |
| CSaneDockingProtocol | |
| CConformerSwitchMover | This mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction |
| CConformerSwitchMoverCreator | |
| CDockingEnsemble | This mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction |
| CDockingEnsemblePrepackProtocol | |
| CDockingHighRes | |
| CDockingHighResFactory | DockingHighResFactory uses the MoverFactory to create instances of DockingHighRes |
| CDockingHighResFilter | High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given (2) interface_score must be negative |
| CDockingHighResLegacy | This mover does the high resolution refinement stage of the RosettaDock algorithm |
| CDockingHighResLegacyCreator | |
| CDockingInitialPerturbation | This mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options |
| CDockingInitialPerturbationCreator | |
| CDockingLowRes | |
| CDockingLowResEnsemble | |
| CDockingLowResFilter | Low-resolution (centroid-mode) filter for docking. Checks (1) at least some contact is being made between docking partners, (2) clashes are limited so partners are not overlapping and (3) constraints, if present, are met |
| CDockingPrepackProtocol | |
| CDockingPrepackProtocolCreator | |
| CDockingProtocol | This is the standard RosettaDock protocol |
| CDockingProtocolCreator | |
| CDockingSlideIntoContact | Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently) |
| CDockMCMCycle | |
| CDockMCMProtocol | |
| CDockMCMProtocolCreator | |
| CDockMinMover | |
| CDockMinMoverCreator | |
| CDockSetupMover | Allows docking using simulated or parallel tempering |
| CDockSetupMoverCreator | |
| CDockTaskFactory | |
| CEllipsoidalRandomizationMover | |
| CFaDockingSlideIntoContact | Slides docking partners together by monitoring fa_rep |
| CInterfaceSidechainMinMover | |
| CRigidBodyInfo | |
| CSidechainMinMover | |
| CSlideIntoContact | More general function for low-res or highres DockingSlideIntoContact |
| CTemperedDocking | Allows docking using simulated or parallel tempering |
| CTemperedDockingCreator | |
| ►Ndomain_assembly | |
| CAddAssemblyConstraints | |
| CAssembleLinkerMover | |
| CCombineChainsMover | |
| CPostDockAssemblyScorer | |
| ►Nelectron_density | |
| CBfactorFittingMover | Mover to fit B factors |
| CBfactorFittingMoverCreator | |
| CBfactorMultifunc | Bfactor multifunc |
| CDensitySymmInfo | Scale density map intensities to match a pose's |
| CDockIntoDensityMover | The workhorse |
| CPointScoreComparator | |
| CRBfitResult | |
| CRBfitResultComparitor | |
| CRefinementResult | |
| CRefinementResultComparitor | |
| CReportFSC | Scale density map intensities to match a pose's |
| CReportFSCCreator | |
| CResultDB | |
| CScaleMapIntensities | Scale density map intensities to match a pose's |
| CScaleMapIntensitiesCreator | |
| CScoredPoint | |
| CScoredPointCmptr | |
| CSetupForDensityScoringMover | |
| CSetupForDensityScoringMoverCreator | |
| CVoxelSpacingMultifunc | Bfactor multifunc |
| CVoxelSpacingRefinementMover | Mover to fit B factors |
| CVoxelSpacingRefinementMoverCreator | |
| ►Nenvironment | |
| ►Nclaims | |
| CClaimStrength | |
| CCutBiasClaim | |
| CCutBiasElement | |
| CCutElement | |
| CDOFElement | |
| CEnvClaim | |
| CEnvLabelSelector | |
| CJumpClaim | |
| CJumpElement | |
| CResidueElement | |
| CTorsionClaim | |
| CVirtResClaim | |
| CXYZClaim | |
| CAutoCutData | |
| CAutoCutDataCreator | |
| CClientMover | |
| CComparator | A brief comparator object initialized with the correct strength accessor for reuse of setup_passports |
| CCoMTrackerCM | |
| CCoMTrackerCMCreator | |
| CDofUnlock | |
| ►CEnvClaimBroker | |
| CBrokeredJumpData | Inner class for tracking the properties of jumps that've been brokered |
| CBrokerResult | |
| CEnvironment | |
| CEnvMover | |
| CEnvMoverCreator | |
| CEXCN_Env_Passport | |
| CEXCN_Env_Security_Exception | |
| CProtectedConformation | |
| CScriptCM | |
| CScriptCMCreator | |
| ►Nenzdes | |
| CAddLigandMotifRotamers | |
| CAddLigandMotifRotamersOperationCreator | |
| CAddOrRemoveMatchCsts | A simple wrapper to get the functionality in EnzConstraintIO into mover format |
| CAddOrRemoveMatchCstsCreator | |
| CAddRigidBodyLigandConfs | |
| CAddRigidBodyLigandConfsCreator | |
| CApplyRandomStoredRBConf | For every ligand that has additional stored rb conformations in the enzdes cacheable observer, the one currently in the pose gets exchanged with a random stored one |
| CBackboneSampler | |
| CBackboneSamplerCreator | |
| CDesignVsNativeComparison | Class that holds a bunch of native poses and compares them |
| CDetectProteinLigandInterface | Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a packing task to set residues within alpha carbons within cut1 of a ligand (or within cut2 with beta carbons facing inwards) to redesign, and within cut3 (or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided, only do the detection for those residues set to AUTO in the resfile |
| CDetectProteinLigandInterfaceOperationCreator | |
| CDiffAtomSasaFilter | |
| CDiffAtomSasaFilterCreator | |
| CDiversifyStoredRBConfs | Uses a docking mover to diversiy the stored confs until they're all min_rms_ away from each other note: no scorefunction used here |
| CEnzdesBaseProtocol | |
| CEnzdesConstraintReporter | |
| CEnzdesFixBBProtocol | |
| CEnzdesFlexBBProtocol | |
| CEnzdesFlexibleRegion | |
| CEnzdesJobInputter | |
| CEnzdesJobInputterCreator | |
| CEnzdesJobOutputter | For now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb SML Feb 4 2016 note. I moved most of PDBJobOutputter into an intermediate class wwPDBJobOutputter to share functions with mmCIFJobOutputter. This class is not being modified (doesn't appear to need it). Its use of dump_pdb forces that function to be protected rather than private |
| CEnzdesJobOutputterCreator | |
| CEnzdesScorefileFilter | |
| CEnzdesScorefileFilterCreator | |
| CEnzRepackMinimize | |
| CEnzRepackMinimizeCreator | |
| CEnzScoreFilter | |
| CEnzScoreFilterCreator | |
| CGenerateStoredRBConfs | Generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used |
| CLigBurialFilter | |
| CLigBurialFilterCreator | |
| CLigDSasaFilter | |
| CLigDSasaFilterCreator | |
| CLigInterfaceEnergyFilter | |
| CLigInterfaceEnergyFilterCreator | |
| CMinimizeStoredRBConfs | Rotamer trials/minimizes each of the ligand conformations stored in the enzdes cacheable observer and overwrites them with the minimized position. if the new, minimized position is too close to one that already exists, a random small perturbation is applied to ensure diversity note: only jump minimization |
| CModifyStoredRBConfs | Virtual base class that has some common functionality |
| CPackRotamersMoverPartGreedy | Mover that packs the side-chains around a given set of target residues in a greedy fashion, and then packs the rest using the sim annealer |
| CPackRotamersMoverPartGreedyCreator | |
| CPoseFoundResiduesCombination | Helper class to process and output the different found poses |
| CPredesignPerturbMover | |
| CPredesignPerturbMoverCreator | |
| CProteinLigandInterfaceUpweighter | Class to alter a packer task to speficially upweight the protein-ligand interaction energies |
| CProteinLigandInterfaceUpweighterOperationCreator | |
| CRemoveLigandFilter | |
| CRemoveLigandFilterCreator | |
| CRepackLigandSiteWithoutLigandMover | Class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues |
| CRepackWithoutLigandFilter | |
| CRepackWithoutLigandFilterCreator | |
| CResidueConformerFilter | Filter that figures out which rotamer of a given rotamer lib is in the pose at apply time, and can be used to filter on it. supposed to be used for ligands, and for now only tested for them, but should also work with any other residue. can be used for example in specificity redesign, if one wants to divide up a bunch of designs according to the orientation in which they bind the ligand |
| CResidueConformerFilterCreator | |
| CSecondaryMatchProtocol | |
| CSetCatalyticResPackBehavior | Queries the pose cst cache for the catalytic residues, and sets the behavior for them as specified in the cstfile |
| CSetCatalyticResPackBehaviorCreator | |
| CUpdateEnzdesHeaderMover | Mover that updates the enzdes pdb header, for use in cases where catalytic residues may be designed |
| CUpdateEnzdesHeaderMoverCreator | |
| CValueEvaluator | Tiny helper struct for EnzdesScoreFileFilter |
| ►Nenzymatic_movers | |
| CEnzymaticMover | |
| CGlycosyltransferaseMover | |
| CGlycosyltransferaseMoverCreator | MoverCreator allowing the MoverFactory to create a GlycosyltransferaseMover |
| ►Nevaluation | |
| CAlignEvaluator | |
| CEvaluatorCreator | The Creator class is responsible for creating a particular mover class |
| CEvaluatorFactory | Create Evaluator Reporters |
| CEvaluatorRegistrator | This templated class will register an instance of an EvaluatorCreator (class T) with the EvaluatorFactory. It will ensure that no EvaluatorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CMetaPoseEvaluator | |
| CPCA | |
| CPoseEvaluator | |
| CSingleValuePoseEvaluator | |
| CSingleValuePoseEvaluator_Size | |
| CSingleValuePoseEvaluator_SSize | |
| CTimeEvaluator | |
| ►Nfarna | |
| ►Nbase_pairs | |
| CBasePairStep | |
| CRNA_BasePairHandler | |
| ►Nfragments | |
| CFragmentLibrary | |
| CFullAtomRNA_Fragments | |
| CRNA_FragmentHomologyExclusion | |
| CRNA_Fragments | |
| CTorsionSet | |
| ►Nlibraries | |
| CBasePairStepLibrary | |
| CBasePairStepSequence | |
| CBasePairType | |
| CChunkSet | |
| CRNA_ChunkLibrary | |
| CRNA_JumpLibrary | |
| CRNA_LibraryManager | Holds all libraries relevant to FARFAR as CONST copies: |
| CRNA_PairingTemplate | |
| ►Nmovers | |
| CRNA_FragmentMover | The RNA de novo structure modeling protocol |
| CRNA_JumpMover | |
| CRNA_LoopCloser | The RNA de novo structure modeling protocol |
| CRNA_Minimizer | The RNA de novo structure modeling protocol |
| CRNA_Relaxer | The RNA de novo structure modeling protocol |
| ►Noptions | |
| CRNA_BasicOptions | |
| CRNA_DeNovoProtocolOptions | |
| CRNA_FragmentMonteCarloOptions | |
| CRNA_MinimizerOptions | |
| ►Nsecstruct | |
| CRNA_SecStructLegacyInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| ►Nsetup | |
| CRNA_DeNovoParameters | |
| CRNA_DeNovoPoseInitializer | Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and jump changes |
| CRNA_DeNovoSetup | |
| CErraserMinimizerMover | |
| CErraserMinimizerMoverCreator | |
| CFARNA_Optimizer | |
| CMultipleDomainMover | The RNA de novo structure modeling protocol |
| CRNA_DeNovoProtocol | The RNA de novo structure modeling protocol |
| CRNA_FragmentMonteCarlo | |
| CRNAIdealizeMover | Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization |
| CRNAIdealizeMoverCreator | |
| CRNAThreadAndMinimizeMover | Thread a new sequence over a given RNA scaffold and do a little optimization |
| CRNAThreadAndMinimizeMoverCreator | |
| ►Nfeatures | |
| ►NhelixAssembly | |
| CConcurrencyTest | |
| CConcurrencyTestCreator | Creator for the HelixBundleFeatures class |
| CFragmentPair | |
| CHelicalFragment | |
| CHelixBundleFeatures | |
| CHelixBundleFeaturesCreator | Creator for the HelixBundleFeatures class |
| ►Nstrand_assembly | |
| CSandwichFeatures | |
| CSandwichFeaturesCreator | Creator for the SandwichFeatures class |
| CSandwichFragment | |
| CStrandBundleFeatures | |
| CStrandBundleFeaturesCreator | Creator for the StrandBundleFeatures class |
| CStrandFragment | |
| CAtomAtomPairFeatures | |
| CAtomAtomPairFeaturesCreator | Creator for the AtomAtomPairFeatures class |
| CAtomInResidueAtomInResiduePairFeatures | |
| CAtomInResidueAtomInResiduePairFeaturesCreator | Creator for the AtomInResidueAtomInResiduePairFeatures class |
| CAtomTypesFeatures | |
| CAtomTypesFeaturesCreator | Creator for the AtomTypesFeatures class |
| CBatchFeatures | |
| CBetaTurnDetection | |
| CBetaTurnDetectionFeatures | |
| CBetaTurnDetectionFeaturesCreator | Creator for the BetaTurnDetectionFeatures class |
| CChargeChargeFeatures | |
| CChargeChargeFeaturesCreator | Creator for the ChargeChargeFeatures class |
| Cclique_saver | |
| CDatabaseFilter | |
| CDatabaseJobInputter | |
| CDatabaseJobInputterCreator | |
| CDatabaseJobOutputter | |
| CDatabaseJobOutputterCreator | |
| CDdGFeatures | |
| CDdGFeaturesCreator | Creator for the DdGFeatures class |
| CFeaturesReporter | |
| CFeaturesReporterCreator | The Creator class is responsible for creating a particular mover class |
| CFeaturesReporterFactory | Create Features Reporters |
| CFeaturesReporterRegistrator | This templated class will register an instance of an FeaturesReporterCreator (class T) with the FeaturesReporterFactory. It will ensure that no FeaturesReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CGeometricSolvationFeatures | |
| CGeometricSolvationFeaturesCreator | Creator for the GeometricSolvationFeatures class |
| CHBondFeatures | |
| CHBondFeaturesCreator | Creator for the HBondFeatures class |
| CHBondParameterFeatures | |
| CHBondParameterFeaturesCreator | Creator for the HBondParameterFeatures class |
| CHelixCapFeatures | |
| CHelixCapFeaturesCreator | Creator for the HelixCapFeaturesCreator class |
| CInterfaceDdGMover | Calculates ddG of binding |
| CInterfaceDdGMoverCreator | |
| CInterfaceFeatures | Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover. By default, will analyze every interface with and report any that have dSASA > cutoff. Interfaces to report can be set via code or RS |
| CInterfaceFeaturesCreator | Creator for the HBondParameterFeatures class |
| CJobDataFeatures | |
| CJobDataFeaturesCreator | Creator for the JobDataFeatures class |
| CLoopAnchorFeatures | |
| CLoopAnchorFeaturesCreator | Creator for the LoopAnchorFeatures class |
| CModelFeatures | |
| CModelFeaturesCreator | Creator for the ModelFeatures class |
| COrbitalsFeatures | |
| COrbitalsFeaturesCreator | Creator for the OrbitalsFeatures class |
| CPairFeatures | |
| CPairFeaturesCreator | Creator for the PairFeatures class |
| CPdbDataFeatures | |
| CPdbDataFeaturesCreator | Creator for the PdbDataFeatures class |
| CPoseCommentsFeatures | |
| CPoseCommentsFeaturesCreator | Creator for the PoseCommentsFeatures class |
| CPoseConformationFeatures | |
| CPoseConformationFeaturesCreator | Creator for the PoseConformationFeatures class |
| CProteinBackboneAtomAtomPairFeatures | |
| CProteinBackboneAtomAtomPairFeaturesCreator | Creator for the ProteinBackboneAtomAtomPairFeatures class |
| CProteinBackboneTorsionAngleFeatures | |
| CProteinBackboneTorsionAngleFeaturesCreator | Creator for the ProteinBackboneTorsionAngleFeatures class |
| CProteinBondGeometryFeatures | |
| CProteinBondGeometryFeaturesCreator | Creator for the ProteinBondGeometryFeatures class |
| CProteinResidueConformationFeatures | |
| CProteinResidueConformationFeaturesCreator | Creator for the ProteinResidueConformationFeatures class |
| CProteinRMSDFeatures | |
| CProteinRMSDFeaturesCreator | Creator for the ProteinRMSDFeatures class |
| CProteinRMSDNoSuperpositionFeatures | |
| CProteinRMSDNoSuperpositionFeaturesCreator | Creator for the ProteinRMSDNoSuperpositionFeatures class |
| CProteinSilentReport | |
| CProtocolFeatures | |
| CRadiusOfGyrationFeatures | |
| CRadiusOfGyrationFeaturesCreator | Creator for the RadiusOfGyrationFeatures class |
| CReport | |
| CReportToDB | |
| CReportToDBCreator | |
| CResidueBurialFeatures | |
| CResidueBurialFeaturesCreator | Creator for the ResidueBurialFeatures class |
| CResidueConformationFeatures | |
| CResidueConformationFeaturesCreator | Creator for the ResidueConformationFeatures class |
| CResidueFeatures | |
| CResidueFeaturesCreator | Creator for the ResidueFeatures class |
| CResidueGridScoresFeatures | |
| CResidueGridScoresFeaturesCreator | Creator for the ResidueGridScoresFeatures class |
| CResidueScoresFeatures | |
| CResidueScoresFeaturesCreator | Creator for the ResidueScoresFeatures class |
| CResidueSecondaryStructureFeatures | |
| CResidueSecondaryStructureFeaturesCreator | Creator for the ResidueSecondaryStructureFeatures class |
| CResidueTotalScoresFeatures | |
| CResidueTotalScoresFeaturesCreator | Creator for the ResidueTotalScoresFeatures class |
| CResidueTypesFeatures | |
| CResidueTypesFeaturesCreator | Creator for the ResidueTypesFeatures class |
| CRotamerBoltzmannWeightFeatures | |
| CRotamerBoltzmannWeightFeaturesCreator | Creator for the RotamerBoltzmannWeightFeatures class |
| CRotamerFeatures | |
| CRotamerFeaturesCreator | Creator for the RotamerFeatures class |
| CRotamerInitializer | |
| CRotamerRecoveryFeatures | |
| CRotamerRecoveryFeaturesCreator | Creator for the RotamerRecoveryFeatures class |
| CRuntimeFeatures | |
| CRuntimeFeaturesCreator | |
| CSaltBridgeFeatures | |
| CSaltBridgeFeaturesCreator | Creator for the SaltBridgeFeatures class |
| CScoreFunctionFeatures | |
| CScoreFunctionFeaturesCreator | Creator for the ScoreFunctionFeatures class |
| CScoreTypeFeatures | |
| CScoreTypeFeaturesCreator | Creator for the ScoreTypeFeatures class |
| CScreeningFeatures | |
| CScreeningFeaturesCreator | Creator for the ScreeningFeaturesCreator class |
| CSecondaryStructureSegment | |
| CSecondaryStructureSegmentFeatures | |
| CSecondaryStructureSegmentFeaturesCreator | Creator for the SecondaryStructureSegmentFeaturesCreator class |
| CSegment | |
| CSmotifFeatures | |
| CSmotifFeaturesCreator | Creator for the SmotifFeaturesCreator class |
| CStructureFeatures | |
| CStructureFeaturesCreator | Creator for the StructureFeatures class |
| CStructureScoresFeatures | |
| CStructureScoresFeaturesCreator | Creator for the StructureScoresFeatures class |
| ►CTaskOperationFeatures | |
| CTaskop_id_name_factory_ | |
| CTaskOperationFeaturesCreator | Creator for the TaskOperationFeatures class |
| CTopCountOfAllInputs | |
| CTopCountOfEachInput | |
| CTopPercentOfAllInputs | |
| CTopPercentOfEachInput | |
| CTotalScoreFeatures | |
| CTotalScoreFeaturesCreator | |
| CTrajectoryMapFeatures | |
| CTrajectoryMapFeaturesCreator | Creator for the TrajectoryMapFeatures class |
| CTrajectoryReportToDB | |
| CTrajectoryReportToDBCreator | |
| CUnrecognizedAtomFeatures | |
| CUnrecognizedAtomFeaturesCreator | Creator for the UnrecognizedAtomFeatures class |
| CWaterFeatures | |
| CWaterFeaturesCreator | Creator for the WaterFeatures class |
| ►Nfibril | |
| CSetupForFibrilMover | |
| ►Nfilters | |
| CCalculatorFilter | |
| CCalculatorFilterCreator | |
| CCombinedFilter | Used to combine multiple seperate filters into a single filter value |
| CCombinedFilterCreator | |
| CCompoundFilter | Used to define a compound logical statement involving other filters with AND, OR and XOR |
| CCompoundFilterCreator | |
| CContingentFilter | |
| CContingentFilterCreator | |
| CFalseFilter | |
| CFalseFilterCreator | |
| CFilter | |
| CFilterCollection | Wrapper-class that contains a vector1 of Filters |
| CFilterCreator | Abstract base class for a Filter factory; the Creator class is responsible for creating a particular filter class |
| CFilterFactory | |
| CFilterRegistrator | This templated class will register an instance of an FilterCreator (class T) with the FilterFactory. It will ensure that no FilterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CIfThenFilter | Evaluate to a value contingent on the evaluation of another filter |
| CIfThenFilterCreator | |
| CMoveBeforeFilter | Apply a sub-mover prior to calculating a filter value |
| CMoveBeforeFilterCreator | |
| CReplicateFilter | |
| CReplicateFilterCreator | |
| CStochasticFilter | |
| CStochasticFilterCreator | |
| CTimeFilter | |
| CTimeFilterCreator | |
| CTrueFilter | |
| CTrueFilterCreator | |
| ►Nfldsgn | |
| ►Nfilters | |
| CCoreDunbrackFilter | |
| CCoreDunbrackFilterCreator | |
| CFragQualFilter | |
| CFragQualFilterCreator | |
| CHelixBendFilter | Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry |
| CHelixBendFilterCreator | |
| CHelixKinkFilter | |
| CHelixKinkFilterCreator | |
| CHelixPairingFilter | |
| CHelixPairingFilterCreator | |
| CHSSTripletFilter | |
| CHSSTripletFilterCreator | |
| CInterlockingAromaFilter | |
| CInterlockingAromaFilterCreator | |
| CNcontactsFilter | |
| CNcontactsFilterCreator | |
| CParallelBetaPairingPreferenceFilter | |
| CParallelBetaPairingPreferenceFilterCreator | |
| CSecondaryStructureCountFilter | |
| CSecondaryStructureCountFilterCreator | |
| CSecondaryStructureFilter | |
| CSecondaryStructureFilterCreator | |
| CSecondaryStructureHasResidueFilter | |
| CSecondaryStructureHasResidueFilterCreator | |
| CSheetTopologyFilter | |
| CSheetTopologyFilterCreator | |
| CStrandCurvatureByLevels | Newer version of filter used in Marcos & Basanta et al. 2017 |
| CStrandCurvatureByLevelsCreator | |
| CStrandHelixGeometryFilter | Another filter used in Marcos & Basanta et al. 2017 that needs to be updated |
| CStrandHelixGeometryFilterCreator | |
| ►Npotentials | |
| ►Nsspot | |
| CHSPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| CNatbiasHelicesSheetPotential | |
| CNatbiasHelixPairPotential | |
| CNatbiasSecondaryStructureEnergy | NatbiasSecondaryStructureEnergy |
| CNatbiasSecondaryStructureEnergyCreator | |
| CNatbiasStrandPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| CSSPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| CAACompositionEnergy | AACompositionEnergy |
| CAACompositionEnergyCreator | |
| CSetAACompositionPotential | |
| CSetAACompositionPotentialCreator | |
| CSetSecStructEnergies | |
| CSetSecStructEnergiesCreator | |
| ►Ntopology | |
| CBB_Pos | |
| CBetaAlphaBetaMotif | |
| CBetaAlphaBetaMotifSet | |
| CDimerPairing | |
| CDimerPairings | |
| CHelix | |
| CHelixPairing | |
| CHelixPairingSet | |
| CHSSTriplet | |
| CHSSTripletSet | |
| CLoop | |
| CSheet | |
| CSheetFoldTypeManager | |
| CSheetSet | |
| CSS_Base | |
| CSS_Info2 | |
| CStrand | |
| CStrandPairing | |
| CStrandPairingSet | |
| CTripletID | |
| CBluePrintBDR | |
| CBluePrintBDRCreator | |
| CCircularPermutation | |
| CCircularPermutationCreator | |
| CMatchResidues | |
| CMatchResiduesMover | |
| CMatchResiduesMoverCreator | |
| CMyAtom | |
| CNcontactsCalculator | |
| CResiduePair | |
| CSheetConstraintGenerator | |
| CSheetConstraintGeneratorCreator | |
| CSheetRemodelConstraintGenerator | Remodel constraint generator for adding sheet constraints |
| CSheetRemodelConstraintGeneratorCreator | |
| ►Nflexpack | |
| ►Nannealer | |
| CFlexbbSimAnnealer | |
| ►Ninteraction_graph | |
| CFlexbbEdge | |
| CFlexbbIGFactory | |
| CFlexbbInteractionGraph | |
| CFlexbbNode | |
| CFlexbbSparseMatrixIndex | |
| CMinimalistFlexbbEdge | |
| CMinimalistFlexbbInteractionGraph | |
| CMinimalistFlexbbNode | |
| COTFFlexbbEdge | |
| COTFFlexbbInteractionGraph | |
| COTFFlexbbNode | |
| CPrecomputedFlexbbInteractionGraph | |
| ►Nrotamer_set | |
| CFlexbbRotamerSet | |
| CFlexbbRotamerSets | |
| CFlexPacker | |
| COtherContextScoreFunction | |
| ►Nflexpep_docking | |
| CFlexPepDockingAbInitio | |
| CFlexPepDockingFlags | |
| CFlexPepDockingLowRes | |
| CFlexPepDockingPoseMetrics | |
| CFlexPepDockingProtocol | |
| CFlexPepDockingProtocolCreator | |
| ►Nfloppy_tail | |
| CFloppyTailMover | FloppyTail mover |
| ►Nflxbb | |
| CCombinedTaskOperation | |
| CDesignTask | |
| CDesignTask_Layer | |
| CDesignTask_Normal | |
| CFilterStructs | |
| CFilterStructs_Packstat | |
| CFilterStructs_TotalCharge | |
| CFlxbbDesign | |
| CFlxbbDesignCreator | |
| CFlxbbDesignPack | |
| CInterlockAroma | |
| CInterlockAromaCreator | |
| CLayerDesignOperation | |
| CLayerDesignOperationCreator | |
| ►Nforge | |
| ►Nbuild | |
| CBridge | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| CBuildInstruction | Tracks modifications to be made and is capable of making residue length changes on a Pose |
| CBuildManager | Container for managing BuildInstructions |
| CConnectRight | Instruction to connect one Pose onto the right side of another |
| CCountFromLeft | Count starting from interval().left in a BuildInstruction |
| CGrowLeft | Instruction to create an n-side extension |
| CGrowRight | Instruction to create a c-side extension |
| CInterval | Simple struct defining a closed interval of residues [left, right] where left <= right |
| CRelativeConnectRight | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| CRelativeSequencePosition | Computes a position wrt values in given BuildInstruction |
| CSegmentInsert | Insert an external segment flanked by new regions |
| CSegmentRebuild | Instruction to rebuild a segment |
| CSegmentSwap | Instruction to swap a segment with an external segment |
| ►Ncomponents | |
| CBDR | |
| CVarLengthBuild | Component that performs a protocol for user-specified variable length remodeling of protein backbone segments |
| ►Nconstraints | |
| CInverseRotamersCstGeneratorCreator | |
| CInverseRotamersRCG | RemodelConstraintGenerator that creates AmbiguousConstraints for all positions in a remodeled region towards a list of inverse rotamers. For every remodel position/inverse rotamer pair, there will be one MultiConstraint consisting of three CoordinateConstraints. the three coordinate constraints will be between: 1) remodel res N - invrot N coords 2) remodel res Ca - invrot Ca coords 3) remodel res Cb - invrot Cb coords All of these MultiConstraints are combined to form one AmbiguousConstraint. In effect, this RCG should bias the remodel trajectory such that one remodel residue backbone overlays with one inverse rotamer backbone |
| CInvrotTreeCstGeneratorCreator | |
| CInvrotTreeRCG | RemodelConstraintGenerator wrapper that makes the constraints generated by an InvrotTree available in VLB or XML |
| CNtoCConstraintGenerator | |
| CNtoCConstraintGeneratorCreator | |
| CRemoveRemodelCsts | |
| CRemoveRemodelCstsCreator | |
| ►Nremodel | |
| CEXCN_RemoveCstsFailed | |
| CGenericRemodelConstraintGenerator | Generic remodel constraint generator for use with arbitrary ConstraintGenerators |
| CLineObject | |
| CRemodelAccumulator | |
| CRemodelConstraintGenerator | Pure virtual base class |
| CRemodelData | |
| CRemodelDesignMover | |
| CRemodelEnzdesCstModule | |
| CRemodelGlobalFrame | |
| CRemodelLigandHandler | |
| CRemodelLoopMover | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| ►CRemodelMover | |
| Cinstruction_flags | |
| CRemodelMoverCreator | |
| CRemodelRotamerLinks | |
| CRemodelRotamerLinksCreator | |
| CRemodelWorkingSet | |
| CResidueVicinityCstGeneratorCreator | |
| CResidueVicinityInfo | Small helper class for the ResidueVicinityRCG |
| CResidueVicinityRCG | RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions |
| CSegment | |
| ►Nfrag_picker | |
| ►Nnonlocal | |
| CNonlocalFrags | |
| CNonlocalPair | Nonlocal fragment pair |
| ►Nquota | |
| CABEGO_SS_Config | Read a config file for quota selector |
| CABEGO_SS_Map | Single pool used by quota selector |
| CABEGO_SS_Pool | Single pool used by quota selector |
| Cmissing_fraction_sorter_biggest_first | |
| Cquota_limits_sorter_biggest_first | |
| Cquota_limits_sorter_smallest_first | |
| CQuotaCollector | A base class for collecting fragments |
| CQuotaConfig | Read a config file for quota selector |
| CQuotaPool | Single pool used by quota selector |
| CQuotaSelector | Selects a given number of fragments using a quota scheme |
| CSecondaryStructurePool | Single pool used by quota selector |
| ►Nscores | |
| CABEGO_SS_Score | |
| CAdaptiveScoreHistogram | |
| CAmbigCSScore | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CAtomBasedConstraintsScore | A base class for all scoring methods that need atom coordinates |
| CAtomPairConstraintsData | Holds data about a single distance constraint in the form AtomPairConstraintsScore needs |
| CAtomPairConstraintsScore | Scores a fragment with a set of AtomPair constraints |
| CBFactor | BFactor score counts identical residues |
| CCachingScoringMethod | |
| CConstScore | ConstScore adds a constant to the total score for each position |
| CCSScore | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CDihedralConstraintsScore | Scores a fragment with a set of Dihedral constraints |
| CDisulfideDistance | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CDisulfideIdentity | DisulfideIdentity score counts identical residues |
| CFourAtomsConstraintData | Holds data about a single four-body constraint in the form usefull for InterbondAngleScore and DihedralConstraintsScore classes |
| CFragmentAllAtomCrmsd | Scores a fragment by its crmsd to the given reference structure |
| CFragmentChunkCrms | Scores a fragment by its tmscore to the given reference structure |
| CFragmentCrmsd | Scores a fragment by its crmsd to the given reference structure |
| CFragmentCrmsdResDepth | Scores a fragment by its crmsd to the given reference structure |
| CFragmentDME | Scores a fragment by its DME to the given reference structure |
| CFragmentScoreManager | Holds particular score components, weights and calculates the total score for a fragment candidate |
| CFragmentScoreMap | Holds all small scores (score components) for a given fragment |
| CFragmentScoringMethod | Fragment candidate score |
| CGunnCost | |
| CGunnCostScore | Scores a fragment by its crmsd to the given reference structure |
| CGunnTuple | |
| CHydrophobicityProfileSimilarity | Scores a fragment by its hydrophobicity similarity |
| CHydrophobicitySimilarity | Scores a fragment by its hydrophobicity similarity |
| CInterbondAngleScore | Scores a fragment with a set of Dihedral constraints |
| CJCoupling | Scores a fragment by the JCouplings |
| CLAMBEGO_Similarity | Scores a fragment by torsion bin similarity |
| CMakeABEGO_SS_Score | Maker class that produces a new ABEGO_SS_Score object |
| CMakeAmbigCSScore | Maker class that produces a new AmbigCSScore object |
| CMakeAtomPairConstraintsScore | Maker class that produces a new AtomPairConstraintsScore object |
| CMakeBFactor | Maker class that produces a new BFactor object |
| CMakeConstScore | Maker class that produces a new ConstScore object |
| CMakeCSScore | Maker class that produces a new CSScore object |
| CMakeDihedralConstraintsScore | Maker class that produces a new DihedralConstraintsScore object |
| CMakeDisulfideDistance | Matker class that produces a new DisulfideDistance object |
| CMakeDisulfideIdentity | Maker class that produces a new DisulfideIdentity object |
| CMakeFragmentAllAtomCrmsd | Maker class that produces a new FragmentAllAtomCrmsd object |
| CMakeFragmentChunkCrms | Maker class that produces a new FragmentChunkCrms object |
| CMakeFragmentCrmsd | Maker class that produces a new FragmentCrmsd object |
| CMakeFragmentCrmsdResDepth | Maker class that produces a new FragmentCrmsdResDepth object |
| CMakeFragmentDME | Maker class that produces a new FragmentDME object |
| CMakeFragmentScoringMethod | Fragment candidate |
| CMakeGunnCostScore | Maker class that produces a new GunnCostScore object |
| CMakeHydrophobicityProfileSimilarity | Maker class that produces a new HydrophobicityProfileSimilarity object |
| CMakeHydrophobicitySimilarity | Maker class that produces a new HydrophobicitySimilarity object |
| CMakeInterbondAngleScore | Maker class that produces a new InterbondAngleScore object |
| CMakeJCoupling | Matker class that produces a new JCoupling object |
| CMakeLAMBEGO_Similarity | Maker class that produces a new TorsionBin object |
| CMakeMidPhiOut | Matker class that produces a new MidPhiOut object |
| CMakeMidPsiOut | Matker class that produces a new MidPsiOut object |
| CMakePartialSecondarySimilarity | Maker class that produces a new PartialSecondarySimilarity object |
| CMakePCS_FragDistance | Matker class that produces a new PCS_FragDistance object |
| CMakePhi | Maker class that produces a new Phi object |
| CMakePhiPsiRmsd | Matker class that produces a new PhiPsiRmsd object |
| CMakePhiPsiSquareWell | Matker class that produces a new PhiPsiSquareWell object |
| CMakeProfileScore | |
| CMakeProfileScoreBlosum62 | |
| CMakeProfileScoreDistWeight | |
| CMakeProfileScoreL1 | |
| CMakeProfileScoreStructL1 | |
| CMakeProfileScoreSubMatrix | |
| CMakeProlinePhiScore | Maker class that produces a new ProlinePhiScore object |
| CMakePsi | Maker class that produces a new Psi object |
| CMakeRamaScore | Maker class that produces a new RamaScore object |
| CMakeRDCScore | Maker class that produces a new RDCScore object |
| CMakeScoreEValuator | |
| CMakeSecondaryIdentity | Maker class that produces a new SecondaryIdentity object |
| CMakeSecondarySimilarity | Maker class that produces a new SecondarySimilarity object |
| CMakeSequenceIdentity | Maker class that produces a new SequenceIdentity object |
| CMakeSolventAccessibility | Maker class that produces a new SolventAccessibility object |
| CMakeTalosSSSimilarity | Maker class that produces a new TalosSSSimilarity object |
| CMakeTorsionBinSimilarity | Maker class that produces a new TorsionBin object |
| CMidPhiOut | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CMidPsiOut | Scores a fragment by the root mean square deviation of Psi and Psi angles |
| CPartialSecondarySimilarity | Scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster |
| CPCS_FragDistance | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CPhi | Scores a fragment by its predicted phi similarity |
| CPhiPsiRmsd | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CPhiPsiSquareWell | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CProfileScore | Fragment candidate |
| CProfileScoreBlosum62 | Fragment candidate |
| CProfileScoreDistWeight | Fragment candidate |
| CProfileScoreL1 | Fragment candidate |
| CProfileScoreStructL1 | Fragment candidate |
| CProfileScoreSubMatrix | Fragment candidate |
| CProlinePhiScore | ProlinePhiScore score counts identical residues |
| CPsi | Scores a fragment by its predicted psi similarity |
| CPValuedFragmentScoreManager | Holds particular score components, weights and calculates the total score for a fragment candidate |
| CRamaScore | RamaScore score counts identical residues |
| CRDCScore | Scores a fragment by its crmsd to the given reference structure |
| CScoreEValuator | Computes E-Value for a Profile object |
| CSecondaryIdentity | SequenceIdentity score counts how many residues share the same secondary structure |
| CSecondarySimilarity | Scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster |
| CSequenceIdentity | SequenceIdentity score counts identical residues |
| CSolventAccessibility | Scores a fragment by its predicted solvent accessibility |
| CTalosSSSimilarity | Scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster |
| CTorsionBinSimilarity | Scores a fragment by torsion bin similarity |
| CAllowPdbIdFilter | Accepts a chunk based on the pdb id of the source protein |
| CBestTotalScoreSelector | Selects a given number of fragments using a quota scheme |
| CBoundedCollector | Keeps the N best fragments candidates for the final selection |
| CBoundedCollector_CompareTotalScore | |
| CBoundedPriorityQueue | |
| CCandidatesCollector | A base class for collecting fragments |
| CCompareByScoreCombination | Comparator based on the linear combination of some score components |
| CCompareQueryPosition | Comparator based on a sequence position in a query |
| CCompareScoreComponent | Comparator based on one of the score components calculated for fragments |
| CCompareTotalScore | Comparator based on the total score of fragments |
| CCompositeFragmentSelector | Selects fragments by running several selectors |
| CContact | |
| CContactCounts | |
| CCS2ndShift | |
| CCSTalosIO | |
| CCustomScoreSelector | Selects a given number of fragments using a quota scheme |
| CDenyPdbIdFilter | Denies a chunk based on the pdb id of the source protein |
| CDiversifyCrmsdByClustering | Selects fragments by running several selectors |
| CDiversifyCrmsdSelector | Selects fragments by running several selectors |
| CDiversifyDihedralsSelector | Selects fragments by running several selectors |
| CFragmentCandidate | Vector candidate says which X-mer from vall fits to a query sequence |
| CFragmentComparatorBase | |
| CFragmentPicker | The core of the fragment picking machinery |
| CFragmentSelectingRule | Selects a given number of fragments just by selecting the best ones |
| CGrabAllCollector | Keeps all fragments candidates for the final selection |
| CJCouplingIO | |
| CLAMBEGO_IO | |
| CLazySortedVector1 | |
| CPdbIdChunkFilter | |
| CPhiPsiTalosIO | |
| CQuotaDebug | |
| CSidechainContactDistCutoff | Defines sidechain contact distance cutoffs |
| CTorsionBinIO | |
| CVallChunk | Chunk of residues extracted from a vall |
| CVallChunkFilter | Base class for a chunk filtering mechanism |
| CVallProvider | Vector of vall chunks |
| CVallResidue | Class for managing a line of the Vall fragment library |
| ►Nfrags | |
| CFragLib | |
| CRMSVallData | |
| CSingleResidueTorsionFragmentLibrary | Class for collection of fragments for a single residue position |
| CTorsionFragment | Class for single piece of torsion fragment |
| CTorsionFragmentLibrary | Class for classic Rosetta fragment library |
| CTorsionFragmentMover | |
| CVallData | |
| ►Ngeneralized_kinematic_closure | |
| ►Nfilter | |
| CGeneralizedKICfilter | |
| ►Nperturber | |
| CGeneralizedKICperturber | |
| ►Nselector | |
| CGeneralizedKICselector | |
| CGeneralizedKIC | |
| CGeneralizedKICCreator | |
| ►Ngenetic_algorithm | |
| CDiscreteRandomizer | |
| CEntity | |
| CEntityElement | Entity element |
| CEntityElementCreator | Entity element creator |
| CEntityElementFactory | The EntityElementFactory is responsible for instantiating entity elements from strings |
| CEntityElementRegistrator | |
| CEntityElementsEqual | |
| CEntityRandomizer | |
| CFitnessFunction | |
| CGeneticAlgorithm | |
| CGeneticAlgorithmBase | |
| CMutate1Randomizer | |
| CPositionSpecificRandomizer | Different set of choices at each position in Entity's traits |
| CVec1Hash | |
| ►Ngrafting | |
| ►Nsimple_movers | |
| CDeleteRegionMover | Delete a region of a pose. Mover Wrapper to grafting utility function |
| CDeleteRegionMoverCreator | |
| CInsertPoseIntoPoseMover | Insert a whole pose into another. Loops, linkers, whaterver. No modeling here. Wrapper to utility function insert_pose_into_pose |
| CInsertPoseIntoPoseMoverCreator | |
| CKeepRegionMover | Keep a contiguous region of a pose, delete the rest. Re-detect disulfides |
| CKeepRegionMoverCreator | |
| CReplaceRegionMover | Replace a region of residues with another from a pose piece. Wrapper to grafting utility function |
| CReplaceRegionMoverCreator | |
| CAnchoredGraftMover | Grafting class adapted from Steven Lewis' pose_into_pose algorithm |
| CAnchoredGraftMoverCreator | |
| CCCDEndsGraftMover | General purpose Grafting class which: 1) superimposes the insert onto the scaffold using any overhang residues, 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the isertion will occur between. 3) Cycles of: a) SmallMover for sampling (Can be disabled)) b) CCDs both terminal ends of the scaffold using flexibility settings or movemap To close the graft. c) MinMover to help close the graft through chainbreak terms d) Closure check - will return if closed (Can be disabled) d) MonteCarlo Boltzmann criterion |
| CCCDEndsGraftMoverCreator | |
| CGraftMoverBase | Fairly abstract base class for GraftMover classes |
| ►Nhbnet | |
| Ccompare_hbond_residues | |
| Ccompare_hbond_resnums | |
| Ccompare_net_vec | |
| CConstrainHBondNetwork | Sets allowed residue types to constrain HBNet residues in downstream design; add this Taskop to any design movers downstream of HBNet |
| CConstrainHBondNetworkCreator | |
| CHBNet | |
| CHBNetCreator | |
| CHBNetStapleInterface | |
| CHBNetStapleInterfaceCreator | |
| Chbond_net_struct | Struct that contains info needed for hbond networks |
| Chbond_res_struct | Struct that represents minimal info for residue in an h-bond network |
| ►Nhelical_bundle | |
| ►Nparameters | |
| CBundleParameters | Parameters class, used to store sets of parameters for parametric backbone generation |
| CBundleParametersSet | BundleParametersSet class, used to store sets of parameters for parametric helical bundle generation |
| CBackboneGridSampler | |
| CBackboneGridSamplerCreator | |
| CBackboneGridSamplerHelper | BackboneGridSamplerHelper class, which stores options for the PerturbBundle mover |
| CBundleGridSampler | |
| CBundleGridSamplerCreator | |
| CBundleGridSamplerHelper | BundleGridSamplerHelper class, which stores options for the PerturbBundle mover |
| CBundleReporterFilter | |
| CBundleReporterFilterCreator | |
| CFitSimpleHelix | |
| CFitSimpleHelixCreator | |
| CFitSimpleHelixMultiFunc | Multifunction class for fitting a simple (straight) helix to the Crick parameters |
| CMakeBundle | |
| CMakeBundleCreator | |
| CMakeBundleHelix | |
| CMakeBundleHelixCreator | |
| CPerturbBundle | |
| CPerturbBundleCreator | |
| CPerturbBundleHelix | |
| CPerturbBundleHelixCreator | |
| CPerturbBundleOptions | PerturbBundleOptions class, which stores options for the PerturbBundle mover |
| ►Nhelix_capper | |
| CHelixNCapperMover | |
| ►Nhotspot_hashing | |
| ►Nmovers | |
| CPlaceProbeMover | |
| CPlaceSurfaceProbe | |
| CPlaceSurfaceProbeCreator | |
| CAddSearchPatternRotSetOp | |
| CCartesianSearchPattern | |
| CComposeSearchPatterns | |
| CConstPattern | |
| CHotspotStub | |
| CHotspotStubSet | |
| CLSMSearchPattern | |
| CPartitionedSearchPattern | |
| CRotationSearchPattern | |
| CSearchPattern | |
| CSearchPatternExpansion | |
| CSearchPatternRotSetOp | |
| CSearchPatternTransform | |
| CSICPatternAtTransform | |
| CSphericalRotationSearchPattern | |
| CStubGenerator | |
| CSurfaceSearchPattern | |
| CTestPattern | |
| CVectorPair | |
| ►Nhybridization | |
| CAllResiduesChanged | (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values |
| CBackboneTorsionPerturbation | |
| CBackboneTorsionPerturbationCreator | |
| CBackboneTorsionSampler | |
| CBackboneTorsionSamplerCreator | |
| CCartesianHybridize | |
| CCartesianSampler | |
| CCartesianSamplerCreator | |
| CChunkTrialMover | |
| CDDomainParse | |
| CDomainAssembly | |
| CFoldTreeHybridize | |
| CFragmentBiasAssigner | |
| ChConvergenceCheck | |
| CHybridizeFoldtreeDynamic | |
| CHybridizeProtocol | |
| CHybridizeProtocolCreator | |
| CInsertChunkMover | |
| CMRMover | |
| CTemplateHistory | |
| CTMalign | |
| CWeightedFragmentSmoothTrialMover | |
| CWeightedFragmentTrialMover | |
| ►Nidealize | |
| CIdealizeMover | Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points |
| CIdealizeMoverCreator | |
| ►Nindel | |
| CIndelOptimizationMover | |
| ►Nindexed_structure_store | |
| ►Nfilters | |
| CFragmentLookupFilter | |
| CFragmentLookupFilterCreator | |
| ►Njd2 | |
| ►Narchive | |
| CAbstractArchiveBase | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| CArchiveBase | |
| CArchiveManager | ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY |
| CBaseArchiveManager | ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY |
| CBatch | Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive |
| CEvaluatedArchive | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| CEXCN_Archive | |
| ►CMPIArchiveJobDistributor | JobDistributor for the iterative ArchiveManager/Archive Framework |
| CCompletionMessage | CompletionMessage(s) are send to the ArchiveManager whenever more than nr_notify decoys have been finished / or when the full batch is finished |
| CNormalizedEvaluatedArchive | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| CSortPredicate | |
| CVarianceStatisticsArchive | |
| ►Nparser | |
| CBluePrint | |
| CDataLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CDataLoaderCreator | A class for creating new instances of DataLoaders for use in the XML Parser |
| CDataLoaderFactory | A factory for creating DataLoaders, which are able to load arbitrary data into the basic::datacache::DataMap used in the XML-based parser. This factory supports the load-time registration scheme allowing DataLoaders to be defined in libraries outside of protocols.lib |
| CDataLoaderRegistrator | This templated class will register an instance of an DataLoaderCreator (class T) with the DataLoaderFactory. It will ensure that no DataLoaderCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CFragmentReader | |
| CFragSetLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CFragSetLoaderCreator | |
| CMonteCarloLoader | The MonteCarloLoader will create named MonteCarlo objects and load them into the basic::datacache::DataMap |
| CMonteCarloLoaderCreator | |
| CResidueSelectorLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CResidueSelectorLoaderCreator | |
| CScoreFunctionLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CScoreFunctionLoaderCreator | |
| CTaskOperationLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CTaskOperationLoaderCreator | |
| CAtomTreeDiffJobInputter | |
| CAtomTreeDiffJobInputterCreator | |
| CAtomTreeDiffJobOutputter | |
| CAtomTreeDiffJobOutputterCreator | |
| CBatchJobInputter | |
| CBOINCJobDistributor | |
| CCompareTags | |
| CDebugOut_MpiFileBuffer | |
| CEnsembleJobInputter | A Job Inputter for distributing a job based on a set of input structures that make up an ensemble Two modes. Seed Ensemble and Grid Ensemble |
| CEnsembleJobInputterCreator | |
| CFileJobOutputter | |
| CFileSystemJobDistributor | |
| CInnerJob | |
| CInnerMultiThreadingJob | |
| CJD2ResourceManager | The JD2ResourceManager is the ResourceManager that should be used when running protocols under the jd2 JobDistributor |
| CJD2ResourceManagerCreator | The JD2ResourceManagerCreator is responsible for instantiating the JD2ResourceManager for the ResourceManagerFactory |
| CJD2ResourceManagerJobInputter | The JD2ResourceManagerJobInputter works with the JobDistributor to define the set of jobs that are to be executed. It reads the list of jobs and the set of resouces they require from one or more XML files |
| CJD2ResourceManagerJobInputterCreator | JD2ResourceManagerJobInputterCreator is responsible for instantiating the JD2ResourceManagerJobInputter for the JobDistributorFactory |
| CJob | |
| CJobDistributor | |
| CJobDistributorFactory | |
| CJobInputter | The JobInputter class is responsible for |
| CJobInputterCreator | Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class |
| CJobInputterFactory | |
| CJobInputterRegistrator | This templated class will register an instance of an JobInputterCreator (class T) with the JobInputterFactory. It will ensure that no JobInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CJobOutputter | |
| CJobOutputterCreator | Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class |
| CJobOutputterFactory | |
| CJobOutputterObserver | |
| CJobOutputterRegistrator | This templated class will register an instance of an JobOutputterCreator (class T) with the JobOutputterFactory. It will ensure that no JobOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CJobsContainer | |
| CLargeNstructJobInputter | |
| CLargeNstructJobInputterCreator | |
| CLazySilentFileJobInputter | |
| CLazySilentFileJobInputterCreator | |
| CmmCIFJobOutputter | |
| CmmCIFJobOutputterCreator | |
| CMpiFileBuffer | |
| CMPIFileBufJobDistributor | |
| CMPIMultiCommJobDistributor | |
| CMPIWorkPartitionJobDistributor | |
| CMPIWorkPoolJobDistributor | |
| CMSDJobDistributor | |
| CMultiThreadingJob | |
| CNoOutputJobOutputter | |
| CNoOutputJobOutputterCreator | |
| CParser | |
| CPDBJobInputter | |
| CPDBJobInputterCreator | |
| CPDBJobOutputter | |
| CPDBJobOutputterCreator | |
| CPoseInputStreamJobInputter | |
| CPoseInputStreamJobInputterCreator | |
| CScoreOnlyJobOutputter | |
| CScoreOnlyJobOutputterCreator | |
| CScreeningJobInputter | |
| CScreeningJobInputterCreator | |
| CShuffleFileSystemJobDistributor | |
| CSilentFileJobInputter | |
| CSilentFileJobInputterCreator | |
| CSilentFileJobOutputter | |
| CSilentFileJobOutputterCreator | |
| CSingleFileBuffer | |
| CWriteFileSFB | |
| CWriteOut_MpiFileBuffer | |
| CwwPDBJobOutputter | |
| ►Njd3 | |
| ►Ndeallocation | |
| CDeallocationMessage | DeallocationMessage class holds the output that's generated by a Job over the course of its execution. The DeallocationMessage is handed by the JobQueen to the JobOutputWriter objects, each of which have the opportunity to pull data out of the DeallocationMessage class |
| CInputPoseDeallocationMessage | InputPoseDeallocationMessage class holds the output that's generated by a Job over the course of its execution. The InputPoseDeallocationMessage is handed by the JobQueen to the JobOutputWriter objects, each of which have the opportunity to pull data out of the InputPoseDeallocationMessage class |
| ►Njob_distributors | |
| CMPIWorkPartitionJobDistributor | |
| CVanillaJobDistributor | The VanillaJobDistributor is a single process running by itself, running a single thread |
| ►Npose_inputters | |
| CPDBPoseInputter | This is the simplest implementation of PoseInputter, which reads from -s/-l and PDB files |
| CPDBPoseInputterCreator | |
| CPoseInputter | The PoseInputter is responsible for reading from the command line a set of structures that are each to be run through a protocol, where each input struture will be the starting point for some number of jobs (where that number is at the JobQueen's discretion). The PoseInputter is responsible for two things: |
| CPoseInputterCreator | |
| CPoseInputterFactory | |
| CPoseInputterRegistrator | This templated class will register an instance of an PoseInputterCreator (class T) with the PoseInputterFactory. It will ensure that no PoseInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CSilentFilePoseInputter | |
| CSilentFilePoseInputterCreator | |
| ►Npose_outputters | |
| CPDBPoseOutputter | The PDBPoseOutputter |
| CPDBPoseOutputterCreator | |
| CPoseOutputter | The PoseOutputter |
| CPoseOutputterCreator | |
| CPoseOutputterFactory | |
| CPoseOutputterRegistrator | This templated class will register an instance of an PoseOutputterCreator (class T) with the PoseOutputterFactory. It will ensure that no PoseOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CScoreFileOutputter | The ScoreFileOutputter |
| CScoreFileOutputterCreator | |
| CSecondaryPoseOutputter | The SecondaryPoseOutputter |
| CSecondaryPoseOutputterCreator | |
| CSecondaryPoseOutputterRegistrator | This templated class will register an instance of an SecondaryPoseOutputterCreator (class T) with the PoseOutputterFactory. It will ensure that no SecondaryPoseOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CSilentFilePoseOutputter | The SilentFilePoseOutputter |
| CSilentFilePoseOutputterCreator | |
| ►Nstandard | |
| CEnergyJobSummary | |
| CMoverAndPoseJob | |
| CPoseJobResult | |
| CPreliminaryLarvalJob | |
| CStandardInnerLarvalJob | |
| CStandardJobQueen | The StandardJobQueen is meant to handle the most common form of Rosetta jobs where a protocol is applied to a single input structure to generate a single output structure. Most JobQueens in Rosetta will to derive from this JobQueen. To make the process of deriving new JobQueens easy, this class's API has been carefully designed to be easy to work with and the class itself has been designed to do as much heavy lifting as possible and to leave only the responsibilities that the StandardJobQueen could not perform to the derived classes |
| CInnerLarvalJob | |
| CJob | protocols::jd3::Job, which is created by the JobQueen from a LarvalJob, is responsible for executing some protocol from beginning to end in its "run" method. It must write all of its output data to the JobResult object that it creates and returns |
| CJobDigraph | A Digraph for storing the relationship between groups of jobs, so that each node in this graph represents a group of jobs, and if the outputs from one group are inputs to another group, then a directed edge from the first group to the second group will be in the graph. The JobDistributor will run all of the jobs in the first group before any of the jobs in the second group will start |
| CJobDigraphUpdater | This class defines the set of operations that a JobQueen can perform to update the JobDigraph that she originally gave to the JobDistributor. In particular, the JobQueen may only update the JobDigraph by adding new nodes to the graph (which will receive incrementally larger indexes) and then adding edges to the graph such that the head node for the edge must land on one of the newly added nodes in the graph. The JobDistributor will hand the JobQueen a JobDigraphUpdater through the JobQueen's update_job_digraph method, and in this call, the JobQueen may add as many nodes as she wishes, and as many edges that land on those new nodes, but when the method exits, those nodes petrify: the JobQueen may not add any more edges that land on those new nodes |
| CJobDirectedEdge | A run-of-the-mill directed edge to use in JobDigraphs |
| CJobDirectedNode | A node to use in JobDigraphs that holds information about how much work has completed for the set of jobs that it represents |
| CJobDistributor | OK – I don't know what the division of labor between a JobDistributor base class and a JobDistributor subclass, so I'm just going to start writing a simple JobDistributor and then follow it by writing an MPI job distributor and then I'll see what shakes out |
| CJobDistributorFactory | |
| CJobGenealogist | The JobGenealogist is meant to manage the annoying / complex / delicate task of keeping track of what jobs belong to which node and what their parents and whether a job has any undiscarded descendants. This task would otherwise fall to the JobQueen, and there are already enough tasks for the JobQueen to manage |
| CJobOutputWriter | JobOutputWriter class is responsible for taking data out of the JobOutput object and writing it to some sort of output destination (a file, or a database) |
| CJobQueen | The JobQueen class (think of a queen bee) has quite a few responsibilities: |
| CJobResult | JobResult class holds the output that's generated by a Job over the course of its execution. The JobResult is handed by the JobQueen to the JobOutputWriter objects, each of which have the opportunity to pull data out of the JobResult class |
| CJobSummary | JobSummary class holds the output that's generated by a Job over the course of its execution. The JobSummary is handed by the JobQueen to the JobOutputWriter objects, each of which have the opportunity to pull data out of the JobSummary class |
| CLarvalJob | protocols::jd3::LarvalJob, which is initialized by the JobQueen, during its intitialize_job_list method, is an immature form of the. It is matured into a Job that can be run by the JobQueen's mature_job method. A LarvalJob may be one of several LarvalJobs that have the same inputs, but differ in their random number seed (i.e. replicates); two jobs that share the same input are meant to point to the same "InnerLarvalJob" to avoid spending too much memory representing identical data |
| CPoseInputSource | The PoseInputSource is a small class for holding data about the starting Pose for a Job and where it comes from (i.e. which of the PoseInputters claims responsibility for creating a Pose for this instance). The "input_tag" is a string description of the input source and will be used as the "job_tag" to control output – the input tag should not include the file extension. It is perfectly reasonable for complex PoseInputters to subclass from PoseInputSource to tuck more complex data in the PoseInputSource, though, the string-string map ought to provide considerable flexibility in storing data without deriving new subclasses |
| ►Njobdist | |
| CAtomTreeDiffJobDistributor | Distributor for use with atomtree_diff silent files |
| CBaseJobDistributor | Coordinates processing of jobs across multiple Rosetta processes |
| CBasicJob | Each Job object describes a particular input to Rosetta |
| CPlainPdbJobDistributor | Distributor for use with plain old PDB files. Use is strongly discouraged in production environments! |
| CPlainRawJobDistributor | Distributor for use with raw files |
| CPlainSilentFileJobDistributor | Distributor for use with silent files |
| ►Njumping | |
| CBaseDisulfPairingLibrary | |
| CBaseJumpSetup | Virtual base class: can create a set of jumps and cuts |
| CBasePairingLibrary | Returns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors |
| CChainbreakDistFunc | |
| CDisulfPairing | |
| CDisulfPairingLibrary | |
| CDisulfTemplate | |
| CInterval | Two numbers, i.e., jump start end residue, or cut-regions.. |
| CJumpSample | |
| ►CJumpSelector | |
| CJumpWeightDef | |
| ►CJumpSetup | |
| CJumpDef | |
| CJumpsFromAllPairings | |
| CMembraneJump | |
| CPairingLibrary | |
| CPairingTemplate | |
| CRandomSheetBuilder | Select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ |
| CResiduePairJump | |
| ►CResiduePairJumpSetup | |
| CJumpDef | |
| CResiduePairJumpSingle | Single residue component of a ResiduePairJump class |
| CSameStrand | 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, |
| CSheetBuilder | Select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ |
| CSpecificGeometryLibrary | |
| CStandardDisulfPairingLibrary | The StandardDisulfPairingsLibrary initializes itself in its constructor from the sampling/disulfide_jump_database_wip.dat file in the database. Users should not in any circumstance invoke any of its non-const methods that are defined in the subclass. This class ought to be reworked to ensure that it is threadsafe |
| CStandardPairingLibrary | This class is thread-unsafe, though, if perhaps none of its non-const functions were accessible, then it wouldn't be |
| ►Nkinematic_closure | Implementation of the kinematic closure algorithm for sampling protein backbone conformations |
| ►Nperturbers | Algorithms for sampling new backbone torsions |
| CBondAnglePerturber | Resample each backbone bond angle from a gaussian distribution |
| CFragmentPerturber | Pick phi/psi torsions from the given fragment library |
| CIdealizeNonPhiPsi | Set all the non-phi/psi DOFs to ideal values |
| CLogFilePerturber | Read torsion angles, bond angles, and bond lengths from a log file |
| COmegaPerturber | |
| CPerturber | Base class for all of the perturber algorithms |
| CPerturberSet | Maintain a set of perturbers to be executed together |
| CRama2bPerturber | Pick phi/psi pairs from the neighbor-dependent rama distribution |
| CRamaPerturber | Pick phi/psi pairs from the rama distribution |
| CUniformPerturber | Sample backbone torsions from a uniform distribution |
| CVicinityPerturber | Limit sampling to phi/psi pairs within some distance of a target loop |
| CWalkingBondAnglePerturber | Resample each backbone bond angle from a gaussian distribution |
| CWalkingPerturber | Make small perturbations to the previous backbone torsions |
| ►Npivot_pickers | Algorithms for choosing pivot residues |
| CEndToEndPivots | Pick pivots that span the entire loop to sample |
| CFixedOffsetPivots | Randomly pick pivots which are always offset by the same amount, but which can appear anywhere in the loop |
| CFixedPivots | Use a fixed set of pivots specified in advance |
| CLoopPivots | Use the start, stop, and cut points of the given loop as pivots |
| CPivotPicker | Base class for all the pivot picking algorithms |
| CStandardPivots | Randomly pick pivots in a way that may or may not span the whole loop |
| ►Nsolution_pickers | Algorithms for picking one of the 0 to 16 solutions generated by kinematic closure |
| CFilteredSolutions | Apply rama and bump checks to quickly filter out bad solutions |
| CRandomSolutions | Pick a completely random solution to return |
| CSolutionPicker | Base class for all the solution picking algorithms |
| CBalancedKicMover | Make a kinematic closure move that obeys detailed balance |
| ►CClosureProblem | Represent and solve a kinematic closure problem |
| CMemento | Save the current state of the closure problem. This is meant to facilitate undoing rejected perturbations when necessary |
| CClosureSolution | Represent a single solution to a kinematic closure problem |
| CKicMover | Find a new backbone conformation for some region of a protein |
| CKicMoverCreator | |
| ►Nkinmatch | |
| CBruteFunGroupTK | |
| CFunGroupTK | |
| CKinFunGroupTK | |
| CKRSQuery | |
| ►Nligand_docking | |
| ►Nligand_options | |
| CInterface | For each residue is it in the interface, a mobile region or a non-mobile region? |
| CInterfaceInfo | Info for each residue- is it part of the interface and if so, what ligands is it near |
| ►Nrdf | |
| CAtomPairData | Simple struct for storing information needed to compute an RDF interaction |
| CRDFBase | |
| CRDFBinaryHbondCreator | Creator to geneate a new RDFBinaryHbondFunction |
| CRDFBinaryHbondFunction | RDFBinaryHbondFunction returns 1.0 if a pair of atoms are donor and acceptor, 0.0 otherwise |
| CRDFBinaryOrbitalFunction | RDFBinaryOrbitalFunction returns 1 for various orbital pairs and 0 otherwise |
| CRDFBinaryOrbitalFunctionCreator | Creator to geneate a new RDFBinaryOrbitalFunction |
| CRDFChargeCreator | Creator to geneate a new RDFChargeFunction |
| CRDFChargeFunction | RDFChargeFunction computes fa_elec for a pair of atoms |
| CRDFElecCreator | Creator to geneate a new RDFElecFunction |
| CRDFElecFunction | RDFElecFunction computes fa_elec for a pair of atoms |
| CRDFEtableCreator | Creator to geneate a new RDFEtableFunction |
| CRDFEtableFunction | RDFEtableFunction computes fa_sol,fa_rep,fa_atr for a pair of atoms |
| CRDFFunctionCreator | The Creator class is responsible for creating a particular RDF Function class |
| CRDFFunctionFactory | Create RDFFunctions |
| CRDFFunctionRegistrator | This templated class will register an instance of an RDFFunctionCreator (class T) with the RDFFunctionFactory. It will ensure that no FeaturesReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CRDFHbondCreator | Creator to geneate a new RDFHbondFunction |
| CRDFHbondFunction | RDFHbondFunction computes h-bonding energy for a pair of atoms |
| CRDFOrbitalFunction | RDFOrbitalFunction computes the orbital score energies of a pair of atoms |
| CRDFOrbitalFunctionCreator | Creator to geneate a new RDFOrbitalFunction |
| CAddHydrogen | |
| CAddHydrogens | |
| CAddHydrogensCreator | |
| CAtomCountFilter | |
| CAtomCountFilterCreator | |
| CChainExistsFilter | |
| CChainExistsFilterCreator | |
| CCompleteConnectionsFilter | |
| CCompleteConnectionsFilterCreator | |
| CCompoundTranslate | |
| CCompoundTranslateCreator | |
| CComputeLigandRDF | |
| CComputeLigandRDFCreator | |
| CDistributionMap | A singleton class that returns a map of strings to enum types |
| CFinalMinimizer | |
| CFinalMinimizerCreator | |
| CGrowLigand | |
| CGrowLigandCreator | |
| CHBondAcceptorFilter | |
| CHBondAcceptorFilterCreator | |
| CHBondDonorFilter | |
| CHBondDonorFilterCreator | |
| CHeavyAtomFilter | |
| CHeavyAtomFilterCreator | |
| CHighResDocker | |
| CHighResDockerCreator | |
| CHighResEnsemble | |
| CHighResEnsembleCreator | |
| CInterfaceBuilder | |
| CInterfaceBuilderLoader | A class for loading InterfaceBuilders into the XML parser's basic::datacache::DataMap |
| CInterfaceBuilderLoaderCreator | |
| CInterfaceScoreCalculator | |
| CInterfaceScoreCalculatorCreator | |
| CLigand_info | |
| CLigandArea | |
| CLigandAreaLoader | |
| CLigandAreaLoaderCreator | |
| CLigandBaseProtocol | Shared functionality for protocols that dock ligands |
| CLigandDesign | |
| CLigandDesignCreator | |
| CLigandDockMain | |
| CLigandDockProtocol | |
| CMinimizeBackbone | |
| CMinimizeBackboneCreator | |
| CMinimizeLigand | |
| CMolarMassFilter | |
| CMolarMassFilterCreator | |
| CMolecularMassFilter | |
| CMolecularMassFilterCreator | |
| CMoveMapBuilder | |
| CMoveMapBuilderLoader | A class for loading MoveMapBuilders into the XML parser's basic::datacache::DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder |
| CMoveMapBuilderLoaderCreator | |
| CRandomConformerMover | Replace the residue at the given position with a randomly selected conformer from its rotamer library |
| CRandomConformers | |
| CRandomConformersCreator | |
| CResidueTorsionRestraints | Manages harmonic restraints on torsions, so they can be turned off for packing |
| CRigidSearchMover | An optimized mover for Monte Carlo trial of rigid body perturbations |
| CRotate | |
| CRotate_info | |
| CRotateCreator | |
| CRotates | |
| CRotatesCreator | |
| CSlideTogether | |
| CSlideTogetherCreator | |
| CStartFrom | |
| CStartFromCreator | |
| CTetherLigand | |
| CTransform | |
| CTransform_info | |
| CTransformCreator | |
| CTransformEnsemble | |
| CTransformEnsemble_info | |
| CTransformEnsembleCreator | |
| CTranslate | |
| CTranslate_info | |
| CTranslateCreator | |
| CUnconstrainedTorsionsMover | Juggles torsional constraints with packing or rotamer trials |
| CWriteLigandMolFile | |
| CWriteLigandMolFileCreator | |
| ►Nloop_build | |
| CLoopBuildMover | |
| CLoopmodelWrapper | |
| CLoopmodelWrapperCreator | |
| CLoopMover_SlidingWindow | LoopMover utilizing fragment insertion, ccd loop closure, and minimization |
| CLoopMover_SlidingWindowCreator | Creator for the LoopMover_SlidingWindowCreator class |
| ►Nloop_modeling | Framework for loop structure prediction |
| ►Nrefiners | Algorithms for lowering loop region scores during sampling |
| CMinimizationRefiner | Refine sampled loops using gradient minimization |
| CMinimizationRefinerCreator | |
| CRepackingRefiner | Refine sampled loops using sidechain repacking |
| CRepackingRefinerCreator | |
| CRotamerTrialsRefiner | Refine sampled loops using rotamer trials |
| CRotamerTrialsRefinerCreator | |
| ►Nsamplers | Algorithms for generating new loop conformations |
| CLegacyKicSampler | Apply the legacy KinematicMover |
| CLegacyKicSamplerCreator | |
| ►Nutilities | Generally useful loop-sampling meta-algorithms |
| CAcceptanceCheck | Apply an additional Monte Carlo acceptance check |
| CLoopFilter | Apply any filter in the context of a loop modeling simulation |
| CLoopMoverGroup | Manage a collection of loop-sampling algorithms |
| CPrepareForCentroid | Convert a pose to centroid mode for low-resolution loop modeling |
| CPrepareForCentroidCreator | |
| CPrepareForFullatom | Convert a pose to fullatom mode for high-resolution loop modeling |
| CPrepareForFullatomCreator | |
| CLoopBuilder | Build loops from scratch |
| CLoopBuilderCreator | |
| CLoopModeler | Attempt to find the native structure for one or more loops |
| CLoopModelerCreator | |
| CLoopMover | Base class for loop-sampling algorithms |
| CLoopProtocol | Monte Carlo search for low energy loop conformations |
| CLoopProtocolCreator | |
| CToolboxKeys | Key names for data shared between loop movers |
| ►Nloophash | |
| CBackboneDB | |
| CBackboneSegment | |
| CBBData | |
| CBBExtraData | |
| CEXCN_bbdb_Merge_Failed | |
| CEXCN_DB_IO_Failed | |
| CEXCN_Invalid_Hashmap | |
| CEXCN_No_Extra_Data_To_Write | |
| CEXCN_Wrong_DB_Format | |
| CFastGapMover | Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much |
| CFilterBucket | |
| CLeapIndex | The LeapIndex stores information about a particular Leap. It hold the oroiginal high precision rigid body transform and an Index to a Backbone Database (BackboneDB) that has the actual phi psi angles. THe storage of the precise RT takes a lot of space and may be deprecated at some point, since once it is hashed, it is rarely needed and can be recomputed if it is. Note that the length of the loop is not stored either, this is again done for saving memory, as huge lists of Leaps are typically created all with the same length. THe length is stored and handled by the owner of LeapIndex list. The LeapIndex does not store the actual backbone coordinates of the Leap. It merely contains an index (the BackboneIndex) which refers to a serial store of backbone triples (phi,psi, omega) which are stored somewhere else in a BackboneDB. THis is improtant to save memory storage since multiple Leaps cna share the same backbone triple and redundant storage would be hugely wasteful |
| CLegacyLeapIndex | |
| CLocalInserter | |
| CLocalInserter_SimpleMin | |
| CLoopHashDiversifier | |
| CLoopHashDiversifierCreator | |
| CLoopHashLibrary | |
| CLoopHashLibraryLoader | LoopHashLibraryLoader constructs a LoopHashLibrary instance from data provided by the ResourceManager |
| CLoopHashLibraryLoaderCreator | LoopHashLibraryLoaderCreator allows the ResourceLoaderFactory to create a LoopHashLibraryLoader instance |
| CLoopHashLibraryOptions | LoopHashLibraryOptions encapsulates the options associated with LoopHashLibrary resources |
| CLoopHashLibraryOptionsCreator | LoopHashLibraryOptionsCreator allows the ResourceLoaderFactory to create a LoopHashLibraryOptions instance |
| ►CLoopHashMap | Loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates |
| Cby_index | A functor for sort() |
| CLoopHashMoverWrapper | |
| CLoopHashMoverWrapperCreator | |
| CLoopHashRelaxProtocol | |
| CLoopHashSampler | |
| CMover_LoopHashRefine | |
| CMPI_LoopHashRefine | |
| CMPI_LoopHashRefine_Emperor | |
| CMPI_LoopHashRefine_Master | |
| CWorkUnit_LoopHash | |
| ►Nloops | |
| ►Nfilters | |
| CLoopAnalyzerFilter | LoopAnalyzerFilter examines loop structures and packages extra scores into a Job object; maybe you can filter on its "LAM score" (not yet implemented) |
| CLoopAnalyzerFilterCreator | |
| ►Nloop_closure | |
| ►Nccd | |
| CCCDLoopClosureMover | Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent |
| CCCDLoopClosureMoverCreator | CCDLoopClosureMoverCreator allows the MoverFactory to create a CCDLoopClosureMover instance |
| CFASelectSlidingWindowLoopClosure | |
| CLoopClosure | |
| CRamaCheck1B | |
| CRamaCheck2B | |
| CRamaCheckBase | |
| CShortLoopClosure | |
| CSlidingWindowLoopClosure | |
| CWidthFirstSlidingWindowLoopClosure | |
| ►Nkinematic_closure | |
| CBaseTabooPerturber | Taboo-sampling perturber base class, the two variants of which, share much code in common, but interface with separate Ramachandran potentials |
| CKinematicMover | A mover class for performing kinematic loop closure on a peptide segment |
| CKinematicPerturber | Pure virtual base class for KinematicPerturber. KinematicPerturbers determine HOW loops should be perturbed. The base class contains a provision for determining WHERE they should be perturbed: MoveMap sensitivity |
| CKinematicWrapper | |
| CNeighborDependentTabooSamplingKinematicPerturber | Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b) |
| CNeighborDependentTorsionSamplingKinematicPerturber | Neighbor-dependent torsion sampling kinematic perturber – uses rama2b for phi/psi lookup |
| CTabooSamplingKinematicPerturber | Taboo-sampling kinematic perturber (still samples randomly, but only within a specific torsion bin, and the Taboo sampler ensures that this torsion bin is varied in each iteration) |
| CTorsionRestrictedKinematicPerturber | Torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin) |
| CTorsionSamplingKinematicPerturber | Torsion sampling kinematic perturber |
| CTorsionSweepingKinematicPerturber | WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber |
| CVicinitySamplingKinematicPerturber | Vicinity sampling kinematic perturber |
| ►Nloop_mover | |
| ►Nperturb | |
| CLoopMover_Perturb_CCD | |
| CLoopMover_Perturb_CCDCreator | Creator for the LoopMover_Perturb_CCDCreator class |
| CLoopMover_Perturb_KIC | |
| CLoopMover_Perturb_KICCreator | Creator for the LoopMover_Perturb_KICCreator class |
| CLoopMover_Perturb_QuickCCD | LoopMover utilizing fragment insertion, ccd loop closure, and minimization |
| CLoopMover_Perturb_QuickCCD_Moves | |
| CLoopMover_Perturb_QuickCCD_MovesCreator | Creator for the LoopMover_Perturb_QuickCCD_MovesCreator class |
| CLoopMover_Perturb_QuickCCDCreator | Creator for the LoopMover_Perturb_QuickCCDCreator class |
| ►Nrefine | |
| CLoopMover_Refine_Backrub | |
| CLoopMover_Refine_BackrubCreator | Creator for the LoopMover_Refine_BackrubCreator class |
| CLoopMover_Refine_CCD | |
| CLoopMover_Refine_CCDCreator | Creator for the LoopMover_Refine_CCDCreator class |
| CLoopMover_Refine_KIC | |
| CLoopMover_Refine_KICCreator | Creator for the LoopMover_Perturb_KICCreator class |
| CLoopRefineInnerCycle | |
| CLoopRefineInnerCycleContainer | |
| CLoopRefineInnerCycleContainerCreator | Creator for the LoopRefineInnerCycleContainer class |
| CLoopRefineInnerCycleFactory | Create LoopMover Reporters |
| CRepackTrial | |
| CRepackTrialCreator | Creator for the RepackTrial class |
| CShearMinCCDTrial | |
| CShearMinCCDTrialCreator | Creator for the ShearMinCCDTrial class |
| CSmallMinCCDTrial | |
| CSmallMinCCDTrialCreator | Creator for the SmallMinCCDTrial class |
| CIndependentLoopMover | |
| CLoopCM | |
| CLoopCMCreator | |
| CLoopMover | The loop-rebuild protocol |
| ►Nloops_definers | |
| CLoopsDatabaseDefiner | |
| CLoopsDatabaseDefinerCreator | Creator for the LoopsDatabaseDefiner class |
| CLoopsDefiner | |
| CLoopsDefinerCreator | Creator for the LoopsDefiner class |
| CLoopsDefinerFactory | Create LoopsDefiner Reporters |
| CLoopsDefinerLoader | A class for loading Loops data into the XML parser's basic::datacache::DataMap |
| CLoopsDefinerLoaderCreator | |
| CLoopsDefinerRegistrator | This templated class will register an instance of an LoopsDefinerCreator (class T) with the LoopsDefinerFactory. It will ensure that no LoopsDefinerCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CLoopsExplicitDefiner | |
| CLoopsExplicitDefinerCreator | Creator for the LoopsExplicitDefiner class |
| CLoopsFileDefiner | |
| CLoopsFileDefinerCreator | Creator for the LoopsFileDefiner class |
| CEXCN_Loop_not_closed | |
| CFoldTreeFromLoops | |
| CFoldTreeFromLoopsCreator | |
| CGuardedLoopsFromFile | This class ensures that the Loops object that is needed to run any of the various forms of loop modeling is correctly initialized from a Pose. If the residues specified from a loops file have not been resolved into the residue indices for a Pose, then this class will die with an assertion failure |
| CJSONFormattedLoopsFileReader | |
| CLoop | Single loop definition |
| CLoop_lt | Used to sort Loops by start-res |
| CLoopFromFileData | |
| CLoopMoverFactory | Create LoopMover Reporters |
| CLoops | |
| CLoopsFileData | |
| CLoopsFileFallbackConfiguration | LoopsFileFallbackConfiguration provides instructions to the ResourceManager for loading loops_files in the absence of a resource definition file |
| CLoopsFileFallbackConfigurationCreator | LoopsFileFallbackConfigurationCreator allows the ResourceManager to create a LoopsFileIO instance |
| CLoopsFileIO | |
| CLoopsFileLoader | LoopsFileLoader constructs a LoopsFileData instance from data provided by the ResourceManager |
| CLoopsFileLoaderCreator | LoopsFileLoaderCreator allows the ResourceLoaderFactory to create a LoopsFileLoader instance |
| CLoopsFileOptions | LoopsFileOptions ecapsulates the options associated with LoopsFile resources |
| CLoopsFileOptionsCreator | LoopsFileOptionsCreator allows the ResourceLoaderFactory to create a LoopsFileOptions instance |
| CPoseNumberedLoopFileReader | |
| CRationalLoopComparator | Orders loops by start position |
| CSerializedLoop | Bare-bones representation of a loop |
| ►Nmagnesium | |
| CMgHydrater | |
| CMgMinimizer | |
| CMgMonteCarlo | |
| CMgOrbitalFrameFinder | |
| CMgScanner | |
| CMgWaterHydrogenPacker | |
| CSampleGrid | |
| ►Nmake_rot_lib | |
| CCentroidRotNum | |
| CMakeRotLibJob | |
| CMakeRotLibJobInputter | |
| CMakeRotLibJobInputterCreator | |
| CMakeRotLibMover | |
| CMakeRotLibOptionsData | |
| CRotData | |
| Crunning_average_pair | Struct that is used in calc_centroids, values init to zero |
| CTorsionRange | |
| ►Nmatch | |
| ►Ndownstream | |
| CActiveSiteGrid | |
| CAtomAngleSecMatchRPE | RPE to figure out if three atoms are within a given angle atoms need to be set through the parent class add_at_ind function |
| CAtomDihedralSecMatchRPE | RPE to figure out if four atoms are within a given dihedral angle atoms need to be set through the parent class add_at_ind function also checks whether a dihedral is periodic, i.e. multiple minima |
| CAtomDistanceSecMatchRPE | RPE to figure out if two atoms are within a given distance atoms need to be set through the parent class add_at_ind function |
| CAtomGeometrySecMatchRPE | Helper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes |
| CClassicMatchAlgorithm | Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner |
| CDownstreamAlgorithm | A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits |
| CDownstreamBuilder | |
| CGeometrySecMatchRPE | Holds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence when an instance of this class is asked to evaluate two residues |
| Chash_upstream_hit | |
| CLigandConformerBuilder | |
| CRigidLigandBuilder | |
| CScoringSecMatchRPE | |
| CSecMatchEvaluatorFactory | Collection of functions making a single score_function |
| CSecMatchResiduePairEvaluator | Base for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue |
| CSecondaryMatcherToDownstreamResidue | A class for an algorithm. Given a conformation of the downstream partner, the algorithm is responsible for producing a set of hits |
| CSecondaryMatcherToUpstreamResidue | A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits |
| CSecondaryMatchUpstreamResProcessor | A simple class to respond to the UpstreamBuilder's process_hit method and pass on the coordinates to its "owning" SecondaryMatcherToUpstreamResidue object |
| CTargetRotamerCoords | |
| Cus_secmatch_hit_compare | A simple struct to use in list.sort() to ensure that the hits returned by a secondary matcher which has possibly generated upstream hits out-of-order, will return an ordered-hit-list in its build_hits_at_all_positions() method |
| ►Noutput | |
| CBestMatchesCollection | |
| CCloudPDBWriter | Output writer that uses a grouper to group matches and then writes out one pdb file per group, with the different hits from the group in different MODEL sections |
| CDownstreamCoordinateKinemageWriter | |
| CDownstreamRMSEvaluator | In the best of all possible worlds, this class would be sufficiently generic such that I could compare RMS for arbitrary subsets of atoms on the downstream partner, but in my first pass implementation, I'm writing while aiming at the RigidLigandBuilder – 1 residue – and I'll compare all heavy atoms |
| CLimitHitsPerRotamerFilter | |
| CMatchCollisionFilter | |
| CMatchConsolidator | |
| CMatchEvaluator | |
| CMatchFilter | |
| CMatchGrouper | |
| CMatchOutputter | |
| CMatchProcessor | |
| CMatchScoreWriter | |
| COutputWriter | |
| CPDBWriter | |
| CPoseInserter | |
| CPoseMatchOutputWriter | Helper class for the MatcherMover that will put a match into a supplied pose |
| CProcessorFactory | |
| CResidueKinemageWriter | |
| CSameChiBinComboGrouper | |
| CSameRotamerComboGrouper | |
| CSameSequenceAndDSPositionGrouper | Class that groups based on same sequence and proximity of the downstream object (based on rms ) NOTE: right now only the downstream position according to the first geomcst id upstream residue is taken into account |
| CSameSequenceGrouper | Class to group matches that represent the same amino acids at the same launch points. E.g. Two matches that both put a cys at launch point #33, a ser a launch point #42 and another ser at launch point #80 would be grouped together – even if they are different rotamers |
| CSingleDownstreamResidueWriter | Class for writing conformations of the downstream partner in a kinemage description |
| CStateAccumulatingMatchFilter | |
| CUpstreamCollisionFilter | This class is used to detect collisions between the upstream residues and filter out matches that have too much collision. It can perform either hard-sphere collision detection, or score-function (Etable) driven collision detection. Four command-line flags are read by the MatcherTask to initialize this class: match::filter_colliding_upstream_residues match::upstream_residue_collision_tolerance match::upstream_residue_collision_score_cutoff match::upstream_residue_collision_Wfa_atr match::upstream_residue_collision_Wfa_rep match::upstream_residue_collision_Wfa_sol |
| CUpstreamDownstreamCollisionFilter | This class is used to detect collisions between upstream residues and downstream poses |
| CUpstreamHitCacher | |
| CWriteKinemageOutputter | |
| CWriteUpstreamCoordinateKinemage | |
| CWriteUpstreamHitKinemage | |
| ►Nupstream | |
| CBuildSet | A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom |
| CDunbrackSCSampler | Basic class for sidechain sampling that pulls data from the Dunbrack rotamer library. The samples that are returned are the basic rotamers and do not include any expansions by the "ex" flags |
| CFullChiSampleSet | |
| COriginalBackboneBuildPoint | |
| CProteinBackboneBuildPoint | |
| CProteinSCSampler | |
| CProteinUpstreamBuilder | |
| CSampleStrategyData | This class holds all of the data associated with the logic for generating extra samples for a particular chi angle. There are tons of ways concievable to build extra rotamers; the data in this class is intended to group all of that data into one place. This class is not responsible for building extra rotamer samples; that responsibility is given to class FullChiSampleSet |
| CScaffoldBuildPoint | |
| CUpstreamBuilder | |
| CUpstreamResidueProcessor | |
| CUpstreamResTypeGeometry | A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom |
| CAddAllPositionsMPM | MPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere |
| CBfactorMPM | Removes positions at which the bfactors for c-alpha atoms are above a desired cutoff. bfactors stored in the pose pdbinfo are taken. if relative bfactors are used, all bfactors are divided by the largest observed bfactor |
| CBool3DGrid | |
| CBool3DGridKinemageWriter | |
| CBumpGrid | |
| Cdownstream_hit | |
| CHit | |
| CHitHasher | This object hashes hits into 6D voxels. This hash can then be traversed to retrieve the hits that hash to the same voxel (matches!). There are 64 hashes representing the 2^6 ways to perturb the bins in 6D by 1/2 of their bin width |
| CHitNeighborFinder | |
| Cmatch_dspos1 | Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position) |
| Cmatch_lite_equals | |
| Cmatch_lite_hasher | |
| CMatchCounter | Class for counting the number of matches given a particular discretization level |
| CMatcher | |
| CMatcherMover | |
| CMatcherMoverCreator | |
| CMatcherOutputStats | |
| CMatcherTask | |
| CMatchOutputTracker | |
| CMatchPositionModifier | Base class for objects that modify the match positions based on some criterion |
| CNumNeighborsMPM | Removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won't be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward |
| COccupiedSpaceHash | This class keeps track of the active voxels "up until now" with 64 hashes |
| CRemoveNorCTermMPM | Added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching |
| CSecondaryStructureMPM | Removes positions at which the pose does not have the desired secondary structure |
| CTaskOperationMPM | Mpm that will get a task operation as specified in the tag from the TaskOperationFactory, apply the task operation to the pose and every residue that is then set to designing in the task will be a match position |
| Cupstream_hit | |
| CVoxelSetIterator | Helper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers |
| ►Nmatdes | |
| CBuildingBlockInterfaceOperation | |
| CBuildingBlockInterfaceOperationCreator | |
| CClashCheckFilter | |
| CClashCheckFilterCreator | |
| CExtractSubposeMover | |
| CExtractSubposeMoverCreator | |
| CGetRBDOFValues | WARNING WARNING WARNING THIS CLASS USES THE THREAD UNSAFE SymDofMoverSampler AND MAKES ANY PROTOCOL THAT USES THIS CLASS THREAD UNSAFE |
| CGetRBDOFValuesCreator | |
| CInterfacePackingFilter | |
| CInterfacePackingFilterCreator | |
| CMatDesGreedyOptMutationMover | |
| CMatDesGreedyOptMutationMoverCreator | |
| CMatDesPointMutationCalculator | |
| CMotifHitsRotamersOperation | |
| COligomericAverageDegreeFilter | |
| COligomericAverageDegreeFilterCreator | |
| CSchemePlaceMotifsMover | |
| CSchemePlaceMotifsMoverCreator | |
| CSymDofMover | |
| CSymDofMoverCreator | |
| CSymDofMoverSampler | WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST, JOB SPECIFIC DATA AND MAKES EVERY CLASS THAT USES THIS DATA THREAD UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED |
| CSymUnsatHbondFilter | Filters based on an upper bound # of buried unsatisfied polar residues |
| CSymUnsatHbondFilterCreator | |
| ►Nmd | |
| CCartesianMD | |
| CCartesianMDCreator | |
| CConstraint | |
| CMDBase | |
| CMDscheduleData | |
| CRattle | |
| CThermostat | |
| ►Nmedal | |
| CMedalExchangeMover | |
| CMedalMover | |
| ►Nmembrane | |
| ►Nbenchmark | |
| CMakeCanonicalHelix | Creates an ideal a-helix from sequence given a range of residues |
| CMakeCanonicalHelixCreator | |
| CSampleTiltAngles | Calculates the energy at all possible tilt angles (0->180 degrees) |
| CSampleTiltAnglesCreator | |
| ►Ngeometry | |
| CEmbedding | |
| CEmbeddingDef | Embedding Setup Helper Class |
| ►Nsymmetry | |
| CSymmetricAddMembraneMover | |
| CSymmetricAddMembraneMoverCreator | Mover Creator |
| ►Nvisualize | |
| CVisualizeEmbeddingMover | Adds virtual residues to visualize span embeddings of the membrane protein |
| CVisualizeEmbeddingMoverCreator | Mover Creator |
| CVisualizeMembraneMover | Add membrane planes to the pose represented by 2 layers of MEM virtual residues |
| CVisualizeMembraneMoverCreator | Mover Creator |
| CAddMembraneMover | Initialize the RosettaMP framework by adding membrane components to the pose |
| CAddMembraneMoverCreator | Mover Creator |
| CAddMPLigandMover | Add Membrane protein ligand mover |
| CAddMPLigandMoverCreator | Mover Creator |
| CFlipMover | Takes a pose and flips the downstream partner around the axis between the COMs of the partners, projected into the membrane plane. CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!! |
| CFlipMoverCreator | Mover Creator |
| CHelixFromSequence | Generates a (transmembrane) helix from a fasta file containing the sequence |
| CHelixFromSequenceCreator | |
| CMembranePositionFromTopologyMover | Compute the initial position of the membrane based upon sequence or structure |
| CMembranePositionFromTopologyMoverCreator | Mover Creator |
| CMPLipidAccessibility | Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible |
| CMPLipidAccessibilityCreator | |
| CMPMutateRelaxMover | |
| CMPMutateRelaxMoverCreator | Mover Creator |
| CMPQuickRelaxMover | |
| CMPQuickRelaxMoverCreator | Mover Creator |
| COptimizeMembranePositionMover | |
| COptimizeMembranePositionMoverCreator | Mover Creator |
| COptimizeProteinEmbeddingMover | |
| COptimizeProteinEmbeddingMoverCreator | Mover Creator |
| CRandomPositionRotationMover | Random Position Rotation Move |
| CRandomPositionTranslationMover | Random Position Translation Move |
| CRotationMover | Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation. Requires two vectors (old and new) and a point on the new vector around which the rotation takes place. The mover is a general mover but used mainly on membrane proteins. For membrane proteins, the two vectors will be the old and new normal and the point will be the new center. The default jump is going to be the membrane jump, but you can also specify your own. The rotation happens around the axis perpendicular to both vectors with an angle enclosed by both vectors |
| CRotationMoverCreator | Mover Creator |
| CSetMembraneCenterMover | Membrane Position Translation Move |
| CSetMembraneCenterMoverCreator | Mover Creator for membrane translation mover |
| CSetMembraneNormalMover | Membrane Position Rotation Move |
| CSetMembraneNormalMoverCreator | Mover creator for membrane rotation mover |
| CSetMembranePositionMover | Membrane Position Translation-Rotation Mover |
| CSetMembranePositionMoverCreator | Mover Creator for composed RT mover |
| CSpinAroundPartnerMover | |
| CSpinAroundPartnerMoverCreator | Mover Creator |
| CTiltMover | Tilts the downstream partner along the axis between the COMs of the partners |
| CTiltMoverCreator | Mover Creator |
| CTransformIntoMembraneMover | Transform a pose into membrane coordinates based on the current embedding of the protein |
| CTransformIntoMembraneMoverCreator | Mover Creator |
| CTranslationMover | Translation vector can be defined in -mp:setup center flag to translate the new pose to. The mover is a general mover but used mainly on membrane proteins, that's why we use this flag here The default jump is going to be the membrane jump, but you can also specify your own |
| CTranslationMoverCreator | Mover Creator |
| CTranslationRotationMover | Translation and Rotation of a pose. The new position can be defined by the -mp:setup center and normal flags. The mover is a general mover, but used mainly on membrane proteins, that's why we use this flag here. The default jump is going to be the membrane jump, but you can also specify your own. See above for the TranslationMover and the RotationMover |
| CTranslationRotationMoverCreator | Mover Creator |
| ►Nmetal_interface | |
| CAddZincSiteConstraints | Add metalsite geometry constraints to pose |
| CMatchGrafter | |
| CMetalSiteResidue | |
| CZincHeterodimerMover | |
| CZincSiteFinder | |
| ►Nmotif_grafting | ...that lives inside of motif_grafting.. |
| ►Nmovers | ...and belongs to the movers class.. |
| Cmotif2scaffold_data | Structure that contains the motif2scaffold_indexes data in a vector and adds fields for fragment matching information |
| Cmotif2scaffold_indexes | Structure that contains the data of corresponding fragments in the motif and scaffold |
| CMotifGraftCreator | |
| CMotifGraftMover | |
| CMotifMatch | |
| ►Nmotifs | |
| CBuildPosition | |
| CIRCollection | |
| CLigandMotifSearch | |
| CMotif | |
| CMotifDnaPacker | |
| CMotifDnaPackerCreator | |
| CMotifHit | |
| CMotifLibrary | |
| CMotifSearch | |
| CSingleMotif | |
| ►Nmoves | |
| CChangeFoldTreeMover | |
| CCompositionMover | |
| CCycleMover | CycleMover iterates through its vector of Movers one at a time over many calls to apply() |
| CCyclicMover | A simple class for cycling between movers in consecutive calls to apply() |
| CDsspMover | |
| CDsspMoverCreator | |
| CDualMonteCarlo | |
| CEXCN_Converged | |
| CFastLinearFunc | |
| CFilterMover | |
| CFilterReportAsPoseExtraScoresMover | This Mover runs a Filter and dumps the report_sm value to Pose's extra scores (for later JD reporting) |
| CFilterReportAsPoseExtraScoresMoverCreator | |
| CFilterReporterMover | A FilterMover that also calls report() on apply() |
| CGeometricFunc | Ramps rapidly from the starting value to the final value. Not 1 at x=1. Doesn't really finish at (1,1). func(x) = 1 - exp( -1 * x * inv_xval_at_0p5 * 0.6931 ); |
| CIfMover | |
| CIfMoverCreator | |
| CInvGeometricFunc | Ramps slowly from the starting value to the final value Non-zero for x = 0. Doesn't really start at (0,0). func(x) = exp( -1 * ( 1 - x ) / ( 1 - xval_at_0p5 ) * 0.6931 ); |
| CIteratedConvergenceMover | A mover that repeatedly applies a sub-mover (up to a given maximum) until the given filter returns values within a certain delta for a given number of cycles |
| CIteratedConvergenceMoverCreator | |
| CJumpOutMover | |
| CLinearFunc | |
| CMCShowMover | |
| CMonteCarlo | This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics |
| CMonteCarloExceptionConverge | |
| CMonteCarloUtil | MCResetMover applies a monte carlo reset |
| CMoveMapMover | |
| CMover | |
| CMoverApplyingMover | |
| CMoverContainer | |
| CMoverCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| CMoverFactory | |
| CMoverForPoseList | |
| CMoverRegistrator | This templated class will register an instance of an MoverCreator (class T) with the MoverFactory. It will ensure that no MoverCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CMoverStatistics | |
| CNullMover | |
| CPDBDumpMover | |
| CPoseCondition | |
| CProfilerMover | |
| CPyMOLMover | |
| CPyMOLMoverCreator | |
| CPyMOLObserver | |
| CRampingFunc | |
| CRampingMover | |
| CRampingMoverCreator | |
| CRandomMover | RandomMover picks a random move and applies it |
| CRandomMoverCreator | |
| CRepeatMover | A Mover that repeats an input Mover a user-specified number of times |
| CReplicaExchangeMC | |
| CResId | |
| CSequenceMover | A Mover that iterates through a vector of Movers, applying each one sequentially |
| CSimulatedTempering | |
| CStructureRestrictor | |
| CTrialCounter | |
| CTrialMover | A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object |
| ►CUDPSocketClient | PyMOLMover helper class. Handle low level UDP transactions stuff. This is a port of original Python version of UDP socket client written writen for PyRosetta |
| CUUID | Unique id of this socket client |
| CVectorPoseMover | A simple class used for a mover that acts on a vector of poses |
| CWhileMover | |
| ►Nmpi_refinement | |
| CClusterer | |
| CMethodParams | |
| CMPI_Refine_Emperor | |
| CMPI_Refine_Master | |
| CMPI_Refinement | |
| CMultiObjective | |
| CScheduler | |
| CSerial_Refine | |
| CStructAvrgMover | |
| CWorkUnit_bbGauss | |
| CWorkUnit_CombinePose | |
| CWorkUnit_FragInsert | |
| CWorkUnit_KicCloser | |
| CWorkUnit_LoopHash | |
| CWorkUnit_MD | |
| CWorkUnit_NormalMode | |
| CWorkUnit_PartialAbinitio | |
| CWorkUnit_RamaPerturber | |
| CWorkUnit_Relax | |
| CWorkUnit_Sampler | |
| ►Nmultistate_design | |
| CMetricCalculatorFitnessFunction | |
| CMultiStateAggregateFunction | |
| CMultiStateEntity | |
| CMultiStateFitnessFunction | |
| CMultiStatePacker | |
| CPackingState | |
| CPartitionAggregateFunction | |
| CPosType | |
| CPosTypeCreator | |
| CSingleState | |
| CSingleStateEntityData | |
| CSingleStateFitnessFunction | |
| ►Nncbb | |
| ►Noop | |
| COopCreatorMover | |
| COopCreatorMoverCreator | |
| COopDockDesignProtocol | |
| COopDockDesignProtocolCreator | |
| CNcbbDockDesignProtocol | |
| CNcbbDockDesignProtocolCreator | |
| CSecStructFinder | |
| CSecStructFinderCreator | |
| CSecStructMinimizeMover | |
| CSecStructMinimizeMoverCreator | |
| CSecStructMinimizeMultiFunc | Class for fitting a length of secondary structure keeping the same dihedrals |
| ►Nneighbor | |
| CNeighborhood | A class to determine the neighborhood of a set of residues within a pose |
| ►Nnoesy_assign | |
| CCovalentCompliance | WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST JOB-SPECIFIC DATA AND MAKES EVERYTHING THAT RELIES ON IT THREAD-UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED |
| ►CCrossPeak | |
| CSpin | Single dimension of a multidimensional peak, stores putative assignments as indices into Resonance table |
| CCrossPeak3D | |
| CCrossPeak4D | |
| CCrossPeakInfo | Shared information about CrossPeak (one for each proton dimension) |
| CCrossPeakList | |
| CDistanceScoreMover | Maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility) |
| CEXCN_AssignmentNotFound | |
| CEXCN_FileFormat | |
| CEXCN_NoesyAssign | |
| CEXCN_UnknownAtomname | |
| CEXCN_UnknownResonance | |
| CFloatingResonance | |
| CFoldResonance | |
| ►CFragsToAtomDist | |
| CDistanceRecord | |
| CLabelResonance | |
| CMethylNameLibrary | |
| CMethylNames | |
| CNoesyModule | WARNING WARNING WARNING THREAD UNSAFE FOR USING THE COVALENTCOMPLIANCE CLASS IN A NON-CONST WAY |
| CPeakAssignment | Fast access to assignments that are stored in CrossPeak – similar to FragID WARNING WARNING WARNING THREAD UNSAFE. THIS CLASS USES THE FUNCTION covalent_compliance WHICH RELIES ON THREAD-UNSAFE SINGLETON CovalentCompliance |
| CPeakAssignmentParameters | |
| CPeakAssignmentResidueMap | Fast access to assignments by residue number |
| CPeakCalibrator | |
| CPeakCalibratorMap | |
| CPeakFileFormat | |
| CPeakFileFormat_Base | |
| CPeakFileFormat_Sparky | |
| CPeakFileFormat_xeasy | |
| CPeakFileFormat_xpk | |
| CProtonResonance | |
| CResonance | |
| CResonanceList | |
| CStructureDependentPeakCalibrator | |
| CStructureIndependentPeakCalibrator | |
| ►Nnonlocal | |
| CBiasedFragmentMover | |
| CChunk | |
| CHelixRotate | |
| CPolicy | |
| CPolicyFactory | |
| CRegion | |
| CSheetTranslate | |
| CSimpleTreeBuilder | |
| CSingleFragmentMover | |
| CSingleFragmentMoverCreator | |
| ►CSmoothPolicy | |
| CCandidate | |
| CStarTreeBuilder | |
| CTreeBuilder | |
| CTreeBuilderFactory | |
| CUniformPolicy | |
| ►Nnormalmode | |
| CContactStruct | |
| CNormalMode | |
| CNormalModeMinimizer | High-level atom tree minimizer class |
| CNormalModeMinimizerCreator | |
| CNormalModeMultifunc | Atom tree multifunction class |
| CNormalModeRelaxMover | |
| CNormalModeRelaxMoverCreator | |
| ►Noptimize_weights | |
| CConstraintedOptimizationWeightFunc | |
| CDDGBindOptEData | |
| CDDGMutationOptEData | |
| CDGBindOptEData | Score a "bound" and an "unbound" structure, and minimize the squared error between the difference in their scores and the experimental delta_G of binding |
| CIterativeOptEDriver | |
| CNestedEnergyTermDDGMutationOptEData | |
| CNestedEnergyTermPNatAAOptEPositionData | |
| COptEData | |
| COptEMultifunc | OptE mode multifunction class |
| COptEPositionData | |
| COptEPositionDataFactory | |
| COptEVariableExpression | |
| CPNatAAOptEPositionData | |
| CPNatAAOptERotamerData | |
| CPNatLigPoseOptEData | |
| CPNatRotOptEPositionData | |
| CPNatRotOptERotamerData | |
| CPNatStructureOptEData | |
| CPSSMOptEPositionData | |
| CScaleAnnealerTemperatureOperation | |
| CSingleStructureData | |
| CWeightRangeConstraint | |
| CWrappedOptEExpressionCreator | |
| CWrapperOptEMultifunc | OptE mode multifunction class |
| ►Npack_daemon | |
| CBasicSimAnnealerRepacker | |
| CDaemonSet | |
| CDenseIGRepacker | |
| CDoubleDenseIGRepacker | |
| CDynamicAggregateFunction | |
| CDynamicAggregateFunctionDriver | |
| CEntityCorrespondence | |
| CEntityFunc | |
| CEntityFuncExpressionCreator | |
| CEntityHistoryLT | |
| CExpExpression | |
| CFASTER_IG_Repacker | |
| CInSetExpression | Returns "true" if the expression ex evaluates to one of a set of indicated values |
| CIterativeVectorExpression | |
| CLnExpression | |
| CMean | |
| CMPIMultistateFitnessFunction | |
| CMultistateAggregateFunction | |
| CMultistateFitnessFunction | |
| CNPDPropCalculator | |
| CNPDPropCalculatorCreator | |
| CPackDaemon | |
| CPowExpression | |
| CQuickRepacker | |
| CRotamerSubsetRepacker | |
| CStructureFileNames | |
| CSurrogateVariableExpression | Stores the result of the surragate expression as if this expression were a variable, but defers to the root expression for questions of deriviatives and which variables are active (this is not a real variable) |
| CTopEntitySet | |
| CVariableVectorExpression | |
| CVectorExpression | |
| CVectorExpressionCreator | |
| CVectorFunction | |
| CVectorFunction2 | |
| CVMax | |
| CVMaxBy | Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the largest value in expression 1 |
| CVMin | |
| CVMinBy | Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the smallest value in expression 1 |
| ►Npb_potential | |
| CSetupPoissonBoltzmannPotential | |
| CSetupPoissonBoltzmannPotentialCreator | |
| ►Npmut_scan | |
| CAlterSpecDisruptionDriver | |
| CMutant | |
| CMutationData | |
| CPointMutScanDriver | |
| ►Npockets | |
| ►CCCluster | @ Cluster of exemplar points |
| CCxyz | |
| CCClusterSet | @ Set of clusters of exemplar points |
| CComparisonGrid | @ |
| CDarcParticleSwarmMinimizer | |
| CEggshellGrid | @ |
| CElectrostaticpotentialGrid | |
| CFingerprintBase | |
| CFingerprintMultifunc | Atom tree multifunction class |
| CGenPharmacophore | |
| CNonPlaidFingerprint | |
| ►CPCluster | @ Cluster of Pocket points |
| CCxyz | |
| CPClusterSet | @ Set of cluster of pocket points |
| CPlaidFingerprint | |
| CPocketConstraint | This constraint favors creating a pocket suitable for a small-molecule |
| CPocketConstraintCreator | Mover creator for the PocketConstraint constraint |
| CPocketExemplarMultifunc | Pocket multifunction class, does objective function of optimization |
| CPocketGrid | @ |
| Cray_distance_derivs | |
| CSmallMol | |
| Cspherical_coor_triplet | |
| CTargetPocketGrid | @ |
| Ctriplet_and_originnum | |
| CUnionEdge | |
| ►Npose_length_moves | |
| CAnalyzeLoopModeling | |
| CAnalyzeLoopModelingCreator | |
| CChain | |
| Cchain_lt | |
| CConnectChainsMover | |
| CConnectChainsMoverCreator | |
| CFinalRMSDComparator | |
| CFixAllLoopsMover | |
| CFixAllLoopsMoverCreator | |
| CInsertResMover | |
| CInsertResMoverCreator | |
| CNearNativeLoopCloser | |
| CNearNativeLoopCloserCreator | |
| CPossibleLoop | |
| CStubRMSDComparator | |
| ►Npose_reporters | |
| CEnergyReporter | Report the pose score or a specific energy term |
| CEnergyReporterCreator | |
| CFilterReporter | Use a RosettaScripts filter as a reporter |
| CFilterReporterCreator | |
| CRMSDReporter | Report the RMSD between two poses |
| CRMSDReporterCreator | |
| ►Npose_selectors | |
| CAndSelector | AND Selector: select poses that were selected by all child selectors |
| CAndSelectorCreator | |
| CClusterPoseSelector | Cluster poses by some real property as reported by the connected reporter (RMSD, ...) |
| CClusterPoseSelectorCreator | |
| CFilter | Use existing RosettaScripts filter as a post selector |
| CFilterCreator | |
| CLogicalSelector | Logical boolean selector base class |
| COrSelector | OR Selector: select poses that were selected by any child selectors |
| COrSelectorCreator | |
| CTopNByProperty | Select top N poses by a specific pose property |
| CTopNByPropertyCreator | |
| ►Nprotein_interface_design | |
| ►Nfilters | |
| CAtomicContactCountFilter | |
| CAtomicContactCountFilterCreator | |
| CAverageDegreeFilter | |
| CAverageDegreeFilterCreator | |
| CBindingStrainFilter | |
| CBindingStrainFilterCreator | |
| CBoltzmannFilter | |
| CBoltzmannFilterCreator | |
| CClashWithTargetFilter | |
| CClashWithTargetFilterCreator | |
| CDesignableResiduesFilter | |
| CDesignableResiduesFilterCreator | |
| CDisulfideFilter | Filters for structures which could form a disulfide bond across the docking interface |
| CDisulfideFilterCreator | |
| CFilterScanFilter | |
| CFilterScanFilterCreator | |
| CFNatFilter | |
| CFNatFilterCreator | |
| CHbondsToAtomFilter | Returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class |
| CHbondsToAtomFilterCreator | |
| CHbondsToResidueFilter | Returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class |
| CHbondsToResidueFilterCreator | |
| CInterfaceHolesFilter | |
| CInterfaceHolesFilterCreator | |
| CIRmsdFilter | |
| CIRmsdFilterCreator | |
| CLRmsdFilter | |
| CLRmsdFilterCreator | |
| CRelativeSegmentFilter | Returns the residues aligned to a segment on the input pdb to the source pdb |
| CRelativeSegmentFilterCreator | |
| CRmsdFilter | |
| CRmsdFilterCreator | |
| CRmsdSimpleFilter | |
| CRmsdSimpleFilterCreator | |
| CSequenceRecoveryFilter | |
| CSequenceRecoveryFilterCreator | |
| CSpecificResiduesNearInterfaceFilter | |
| CSpecificResiduesNearInterfaceFilterCreator | |
| CSSamountFilter | |
| CSSamountFilterCreator | |
| CStubScoreFilter | |
| CStubScoreFilterCreator | |
| CStubScoreLoopsFilter | |
| CStubScoreLoopsFilterCreator | |
| CTorsion | |
| CTorsionCreator | |
| ►Nmovers | |
| CAddChainBreak | Mover that sets a chainbreak in a specified position |
| CAddChainBreakCreator | |
| CAddSidechainConstraintsToHotspots | |
| CAddSidechainConstraintsToHotspotsCreator | |
| CBackrubDDMover | |
| CBackrubDDMoverCreator | |
| CBestHotspotCstMover | Remove all HotspotCst's from the pose except the best X |
| CBestHotspotCstMoverCreator | |
| CBuildAlaPose | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CBuildAlaPoseCreator | |
| CCoordinateConstraintStack | |
| CDesignMinimizeHbonds | Used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined |
| CDesignMinimizeHbondsCreator | |
| CDisulfideMover | |
| CDisulfideMoverCreator | |
| CDockAndRetrieveSidechains | |
| CDockAndRetrieveSidechainsCreator | |
| CDockWithHotspotMover | A mover to mutate a single residue |
| CDockWithHotspotMoverCreator | |
| CFavorNativeResiduePreCycle | |
| CFavorNativeResiduePreCycleCreator | |
| CFavorNonNativeResiduePreCycle | |
| CFavorNonNativeResiduePreCycleCreator | |
| CHotspotDisjointedFoldTreeMover | |
| CHotspotDisjointedFoldTreeMoverCreator | |
| CHotspotHasherMover | |
| CHotspotHasherMoverCreator | |
| CInterfaceRecapitulationMover | Pure virtual base class for movers which redesign and repack the interface |
| CInterfaceRecapitulationMoverCreator | |
| CLoopFinder | |
| CLoopFinderCreator | |
| CLoopLengthChange | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CLoopLengthChangeCreator | |
| CLoopMoverFromCommandLine | |
| CLoopMoverFromCommandLineCreator | |
| CLoopOver | Essentially the same as the WhileMover but allows parsing and cloning. Will be removed at a future point. This should now be incorporated into WhileMover |
| CLoopOverCreator | |
| CLoopRemodel | |
| CLoopRemodelCreator | |
| CMapHotspot | |
| CMapHotspotCreator | |
| CNucleotideMutation | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CNucleotideMutationCreator | |
| CPatchdockTransform | Wrapper around protocols::protein_interface_design::PatchdockReader class. That class is derived from JobInputter and handles input situations that involve patchdock output files. Here, we provide an entry point for a patchdock transformation within the RosettaScripts trajectory |
| CPatchdockTransformCreator | |
| CPeptideStapleDesignMover | Introduces a peptide staple (ala G. Verdine) to the pose |
| CPeptideStapleDesignMoverCreator | |
| CPlacementAuctionMover | |
| CPlacementAuctionMoverCreator | |
| CPlacementMinimizationMover | Simple rb-minimization in a bb-stub constraint biased forcefield. Note that this mover is dependent on a placement mover for setting its stubsets |
| CPlacementMinimizationMoverCreator | |
| CPlaceOnLoop | |
| CPlaceOnLoopCreator | |
| CPlaceSimultaneouslyMover | Choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria |
| CPlaceSimultaneouslyMoverCreator | |
| CPlaceStubMover | Choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria |
| CPlaceStubMoverCreator | |
| CPrepackMover | |
| CPrepackMoverCreator | |
| CProteinInterfaceMultiStateDesignMover | Wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework |
| CProteinInterfaceMultiStateDesignMoverCreator | |
| CRandomMutation | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CRandomMutationCreator | |
| CRepackMinimize | One round of design/repacking followed by interface sc/bb and rigid-body minimization |
| CRepackMinimizeCreator | |
| CSaveAndRetrieveSidechains | Saves a pose and reapplies its sequence and rotamers at a later stage. The constructor saves the initial pose, and then any calls to apply replace the residues on the input pose with that saved pose. Notice, that only ALA positions will be replaced, so this is meant to work strictly along with BuildAlaPose moves. This way, if in the design process an interface residue is designed, that will not be reverted to w/t |
| CSaveAndRetrieveSidechainsCreator | |
| CSetAtomTree | Mover that sets a user-defined atom tree |
| CSetAtomTreeCreator | |
| CSetTemperatureFactor | Set the temperature (b-)factor column in the PDB according to som filter's value. The filter needs to be ResId-compatible, i.e. to report values on a per-residue basis |
| CSetTemperatureFactorCreator | |
| CSetupHotspotConstraintsLoopsMover | |
| CSetupHotspotConstraintsLoopsMoverCreator | |
| CSetupHotspotConstraintsMover | |
| CSetupHotspotConstraintsMoverCreator | |
| CShoveResidueMover | |
| CShoveResidueMoverCreator | |
| CSpinMover | |
| CSpinMoverCreator | |
| CSubroutineMover | |
| CSubroutineMoverCreator | |
| CTaskAwareCsts | Applies csts (currently only coordinate csts) to every designable position in pose according to taskoperations |
| CTaskAwareCstsCreator | |
| CTopologyBrokerMover | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CTopologyBrokerMoverCreator | |
| CTryRotamers | |
| CTryRotamersCreator | |
| CVLB | User interface for YAB's Variable Length Build |
| CVLBCreator | |
| CDockDesignFilterFactory | |
| CFavorNativeResidue | |
| CFavorNonNativeResidue | |
| CParserJobInputter | |
| CParserJobInputterCreator | |
| CPatchdockReader | |
| CReportPSSMDifferences | |
| CReportSequenceDifferences | |
| CRevert | |
| CTransformation | |
| ►Nqsar | |
| ►Nscoring_grid | |
| CAllAtomNormalization | |
| CAtrGrid | |
| CAtrGridCreator | |
| CChargeAtom | Very light representation of an atom that is just a charge and a cartesian space position |
| CChargeGrid | |
| CChargeGridCreator | |
| CChiAngleNormalization | |
| CClassicGrid | |
| CClassicGridCreator | |
| CConstantScoreBase | |
| CGridBase | |
| CGridCreator | Abstract class fora mover factory. The creator class is responsible for creating a particular mover class |
| CGridFactory | |
| CGridInitMover | |
| CGridInitMoverCreator | |
| CGridManager | |
| CGridRegistrator | This templated class will register an instance of a GridCreator (class T) with the GridFactory. It will ensure that no GridCreator is registered twice and centralizes the registration logic |
| CHbaGrid | |
| CHbaGridCreator | |
| CHbdGrid | |
| CHbdGridCreator | |
| CHeavyAtomNormalization | |
| CLigandPropertyScore | |
| CLigandPropertyScoreCreator | |
| CMolecularWeightNormalization | |
| CRepGrid | |
| CRepGridCreator | |
| CScoreNormalization | |
| CScoringGridLoader | A class for loading ScoringGrids into the XML parser's basic::datacache::DataMap |
| CScoringGridLoaderCreator | |
| CShapeGrid | |
| CShapeGridCreator | |
| CSingleGrid | |
| CSolvationGrid | |
| CSolvationGridCreator | |
| CSolvationMetaGrid | |
| CSolvationMetaGridCreator | |
| CVdwGrid | |
| CVdwGridCreator | |
| CColorGradient | |
| CqsarCreator | |
| CqsarMap | |
| CqsarMover | |
| CqsarOptData | |
| CqsarOptFunc | |
| CqsarPoint | |
| CRenderGridsToKinemage | |
| CRenderGridsToKinemageCreator | |
| ►Nrbsegment_relax | |
| CAutoRBMover | |
| CCCDMoveWrapper | |
| CFragInsertAndAlignMover | Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply' |
| CGaussianRBSegmentMover | |
| CHelicalGaussianMover | |
| CIdealizeHelicesMover | |
| CIdealizeHelicesMoverCreator | |
| CMakeStarTopologyMover | |
| CMakeStarTopologyMoverCreator | |
| COptimizeThreadingMover | |
| COptimizeThreadingMoverCreator | |
| CRB_lt | |
| CRBResidueRange | RB residue range |
| CRBSegment | Rigid-body segments in a protein |
| CRBSegmentMover | Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply' |
| CRBSegmentRelax | |
| CSequenceShiftMover | |
| CStrandTwistingMover | |
| ►Nrecces | |
| ►Noptions | |
| CRECCES_Options | |
| ►Nparams | |
| CRECCES_Parameters | |
| ►Nsampler | |
| ►Nrna | |
| CMC_RNA_KIC_Sampler | |
| CMC_RNA_MultiSuite | |
| CMC_RNA_OneJump | |
| CMC_RNA_Sugar | |
| CMC_RNA_Suite | |
| CMC_Any | |
| CMC_Comb | |
| CMC_Loop | |
| CMC_OneTorsion | |
| CMC_Sampler | |
| ►Nscratch | |
| CThermalMinimizer | Use a simulated tempering simulation to refine a pose |
| CThermalMinimizerCreator | |
| CThermalSamplingMover | Use a simulated tempering simulation to refine a pose |
| CThermalSamplingMoverCreator | |
| CHistogram | |
| CRECCES_Mover | |
| ►Nrelax | |
| ►Nmembrane | |
| CMPFastRelaxMover | |
| CMPFastRelaxMoverCreator | Mover Creator |
| CMPRangeRelaxMover | |
| CAtomCoordinateCstMover | |
| CAtomCoordinateCstMoverCreator | |
| ►CCentroidRelax | Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization |
| Cparameters | Container for ramp settings |
| CClassicRelax | A functor class which implements the classic Rosetta++ pose_relax protocol |
| CClassicRelaxCreator | |
| CFastRelax | |
| CFastRelaxCreator | |
| CLocalRelax | |
| CLocalRelaxCreator | |
| CMiniRelax | |
| CRangeRelaxMover | |
| CRelaxProtocolBase | |
| CRelaxScriptCommand | |
| CSRelaxPose | |
| CWorkUnit_BatchRelax | |
| CWorkUnit_BatchRelax_and_PostRescore | |
| ►Nresidue_optimization | |
| CMetapatchEnumeration | |
| ►Nresidue_selectors | |
| CStoredResidueSubsetSelector | The StoredResidueSubsetSelector 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 |
| CStoredResidueSubsetSelectorCreator | |
| CStoreResidueSubsetMover | Mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls |
| CStoreResidueSubsetMoverCreator | |
| CTaskSelector | The TaskSelector 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 |
| CTaskSelectorCreator | |
| CUnsatSelector | 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) |
| CUnsatSelectorCreator | |
| ►Nrigid | |
| CMembraneCenterPerturbationMover | Perturb the pose along membrane normal |
| CMembraneNormalPerturbationMover | Rotation pose around membrane center, perturb the membrane normal vector relative to the pose |
| CMovePoseToMembraneCenterMover | Move pose into a membrane |
| CRigidBodyDeterministicSpinMover | |
| CRigidBodyDofPerturbMover | This Mover does a perturbation defined by the rotational and translational magnitudes. Allowed dofs are specified by a map. Can be defined through a move map or with rb_jump. A single jump is selected |
| CRigidBodyDofRandomizeMover | A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only |
| CRigidBodyDofRandomTransMover | A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a randomly selected jump |
| CRigidBodyDofSeqPerturbMover | This Mover does a perturbation defined by the rotational and translational magnitudes. Allowed dofs are specified by a map. Can be defined through a move map or with rb_jump. All jumps are selected in random order |
| CRigidBodyDofSeqRandomizeMover | A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only |
| CRigidBodyDofSeqTransMover | A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump. Jumps are visited in random order |
| CRigidBodyDofTransMover | A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump |
| CRigidBodyMotionMover | |
| CRigidBodyMover | Rigid-body random translate/rotate around centroid of downstream side of a jump |
| CRigidBodyPerturbMover | This Mover does a perturbation defined by the rotational and translational magnitudes |
| CRigidBodyPerturbNoCenterMover | Does a perturbation defined by the rotational and translational magnitudes without setting up the center Can be defined through a move map or with rb_jump Defining through a movemap with multiple jumps leads to a random jump being chosen at apply time, NOT at construction time! This is done to simplify docking with more than one active jump |
| CRigidBodyPerturbNoCenterMoverCreator | |
| CRigidBodyPerturbRandomJumpMover | |
| CRigidBodyRandomizeMover | |
| CRigidBodySpinMover | A Mover that spins about a random axis |
| CRigidBodyTiltMover | A Mover that tilts around the spin axis |
| CRigidBodyTiltMoverCreator | |
| CRigidBodyTransMover | This Mover translate down an axis |
| CRigidBodyTransMoverCreator | |
| CRollMover | |
| CRollMoverCreator | |
| CRotateJumpAxisMover | |
| CUniformRigidBodyCM | |
| CUniformRigidBodyCMCreator | |
| CUniformRigidBodyMover | |
| CUniformRigidBodyMoverCreator | |
| CUniformSphereTransMover | Rigid-body move that evenly samples the space within a sphere |
| CWholeBodyRotationMover | Rotate the whole pose |
| CWholeBodyTranslationMover | Translate the whole pose |
| ►Nrosetta_scripts | |
| CAdditionalOutputWrapper | |
| CAdditionalOutputWrapperCreator | |
| CMultipleOutputWrapper | |
| CMultipleOutputWrapperCreator | |
| CMultiplePoseMover | |
| CMultiplePoseMoverCreator | |
| ►CParsedProtocol | |
| CMoverFilterPair | |
| CParsedProtocolCreator | |
| CPosePropertyReporter | |
| CPosePropertyReporterCreator | Abstract base class for a PosePropertyReporter factory; the Creator class is responsible for creating a particular PosePropertyReporter class |
| CPosePropertyReporterFactory | |
| CPosePropertyReporterRegistrator | This templated class will register an instance of an PosePropertyReporterCreator (class T) with the PosePropertyReporterFactory. It will ensure that no PosePropertyReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CPoseSelector | |
| CPoseSelectorCreator | Abstract base class for a PoseSelector factory; the Creator class is responsible for creating a particular PoseSelector class |
| CPoseSelectorFactory | |
| CPoseSelectorRegistrator | This templated class will register an instance of an PoseSelectorCreator (class T) with the PoseSelectorFactory. It will ensure that no PoseSelectorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CRosettaScriptsParser | Reading the xml file and generating the mover |
| CSavePoseMover | Mover that can be used to save or restore a pose at an arbitrary point during a rosetta scripts protocol. other movers or filters can be set up to access poses saved by this mover during their apply calls |
| CSavePoseMoverCreator | |
| ►Nrotamer_recovery | |
| CPerNativeRRReporterHuman | |
| CRotamerRecovery | |
| CRotamerRecoveryFactory | Create Rotamer_Recovery Reporters |
| CRotamerRecoveryMover | |
| CRotamerRecoveryMoverCreator | |
| CRotamerRecoveryRegistrator | This templated class will register an instance of an RotamerRecoveryCreator (class T) with the RotamerRecoveryFactory. It will ensure that no RotamerRecoveryCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CRRComparer | The comparison functionality for the rotamer recovery test |
| CRRComparerAutomorphicRMSD | |
| CRRComparerAutomorphicRMSDCreator | |
| CRRComparerChiDiff | |
| CRRComparerChiDiffCreator | |
| CRRComparerCreator | The Creator class is responsible for creating a particular mover class |
| CRRComparerElecDensDiff | |
| CRRComparerElecDensDiffCreator | |
| CRRComparerRotBins | |
| CRRComparerRotBinsCreator | |
| CRRProtocol | The protocol to run to compute the rotamer recovery the rotamer recovery test |
| CRRProtocolCreator | The Creator class is responsible for creating a particular mover class |
| CRRProtocolMinPack | |
| CRRProtocolMinPackCreator | |
| CRRProtocolMover | |
| CRRProtocolMoverCreator | |
| CRRProtocolPackRotamers | |
| CRRProtocolPackRotamersCreator | |
| CRRProtocolReferenceStructure | |
| CRRProtocolReferenceStructureCreator | |
| CRRProtocolRelax | |
| CRRProtocolRelaxCreator | |
| CRRProtocolRotamerTrials | |
| CRRProtocolRotamerTrialsCreator | |
| CRRProtocolRTMin | |
| CRRProtocolRTMinCreator | |
| CRRReporter | The reporting functionality for the rotamer recovery test |
| CRRReporterCreator | The Creator class is responsible for creating a particular mover class |
| CRRReporterHuman | The reporting functionality for the rotamer recovery test in a human readable format |
| CRRReporterHumanCreator | |
| CRRReporterSimple | |
| CRRReporterSimpleCreator | |
| CRRReporterSQLite | |
| CRRReporterSQLiteCreator | |
| ►NRotamerDump | |
| CRotamerDumpMover | Mover for dumping interaction graph information. The information is appended to the current job |
| ►Nrpc | |
| CBasicCmdLineInit | |
| CBasicInit | |
| CJSON_RPC | |
| ►Nsasa_scores | |
| CPoly | |
| CPPoly | |
| ►Nscoring | |
| ►Nmethods | |
| ►Npcs | |
| CGridSearchIterator | |
| CPCS_data | |
| CPCS_data_input | PCS_data_input contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_input_manager | |
| CPCS_data_per_lanthanides | |
| CPCS_Energy | |
| CPCS_Energy_parameters_manager | |
| CPCS_file_data | PCS_file_data contain all the information of a .npc file one per lanthanide |
| CPCS_line_data | PCS_line_data class: hold a line of the input file information (.npc format) One PCS_line_data per line in the input file |
| CPCS_tensor | |
| CPseudocontactShiftEnergyCreator | |
| CTensorsOptimizer | |
| ►Npcs2 | |
| CGridSearchIteratorCA | |
| CPcsDataCenter | |
| CPcsDataCenterManager | |
| CPcsDataCenterManagerSingleton | |
| CPcsDataLanthanide | |
| CPcsEnergy | |
| CPcsEnergyCreator | |
| CPcsEnergyParameter | |
| CPcsEnergyParameterManager | |
| CPcsGridSearchParameter | |
| CPcsGridSearchParameterManager | |
| CPcsInputCenter | PcsInputCenter contain all the input information for one paramagnetic center. It can contain multiple data set |
| CPcsInputCenterManager | |
| CPcsInputFile | PcsInputFile contain all the information of a .npc file one per lanthanide |
| CPcsInputLine | PcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file |
| CPcsTensor | |
| CTensorsOptimizer | |
| CTensorsOptimizerFix | |
| CTensorsOptimizerSvd | |
| ►NpcsTs1 | |
| CGridSearchIterator_Ts1 | |
| CPCS_data_input_manager_Ts1 | |
| CPCS_data_input_Ts1 | PCS_data_input_Ts1 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts1 | |
| CPCS_data_Ts1 | |
| CPCS_Energy_parameters_manager_Ts1 | |
| CPCS_Energy_Ts1 | |
| CPCS_file_data_Ts1 | PCS_file_data_Ts1 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts1 | PCS_line_data_Ts1 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts1 per line in the input file |
| CPCS_tensor_Ts1 | |
| CPseudocontactShiftEnergyCreator_Ts1 | |
| CTensorsOptimizer_Ts1 | |
| ►NpcsTs2 | |
| CGridSearchIterator_Ts2 | |
| CPCS_data_input_manager_Ts2 | |
| CPCS_data_input_Ts2 | PCS_data_input_Ts2 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts2 | |
| CPCS_data_Ts2 | |
| CPCS_Energy_parameters_manager_Ts2 | |
| CPCS_Energy_Ts2 | |
| CPCS_file_data_Ts2 | PCS_file_data_Ts2 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts2 | PCS_line_data_Ts2 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts2 per line in the input file |
| CPCS_tensor_Ts2 | |
| CPseudocontactShiftEnergyCreator_Ts2 | |
| CTensorsOptimizer_Ts2 | |
| ►NpcsTs3 | |
| CGridSearchIterator_Ts3 | |
| CPCS_data_input_manager_Ts3 | |
| CPCS_data_input_Ts3 | PCS_data_input_Ts3 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts3 | |
| CPCS_data_Ts3 | |
| CPCS_Energy_parameters_manager_Ts3 | |
| CPCS_Energy_Ts3 | |
| CPCS_file_data_Ts3 | PCS_file_data_Ts3 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts3 | PCS_line_data_Ts3 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts3 per line in the input file |
| CPCS_tensor_Ts3 | |
| CPseudocontactShiftEnergyCreator_Ts3 | |
| CTensorsOptimizer_Ts3 | |
| ►NpcsTs4 | |
| CGridSearchIterator_Ts4 | |
| CPCS_data_input_manager_Ts4 | |
| CPCS_data_input_Ts4 | PCS_data_input_Ts4 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts4 | |
| CPCS_data_Ts4 | |
| CPCS_Energy_parameters_manager_Ts4 | |
| CPCS_Energy_Ts4 | |
| CPCS_file_data_Ts4 | PCS_file_data_Ts4 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts4 | PCS_line_data_Ts4 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts4 per line in the input file |
| CPCS_tensor_Ts4 | |
| CPseudocontactShiftEnergyCreator_Ts4 | |
| CTensorsOptimizer_Ts4 | |
| ►Nsaxs | |
| CPDDFEnergy | |
| CPDDFEnergyCreator | |
| CEnsembleEnergy | |
| CEnsembleEnergyCreator | |
| CInterchainEnvEnergy | |
| CInterchainEnvEnergyCreator | |
| CInterchainPairEnergy | |
| CInterchainPairEnergyCreator | |
| CResidualDipolarCouplingEnergyRigidSegments | |
| CResidualDipolarCouplingEnergyRigidSegmentsCreator | |
| CSpecialRotamerEnergy | |
| CSpecialRotamerEnergyCreator | |
| CImplicitFastClashCheck | |
| CInterchainPotential | Singleton class to hold the interface-derived statistics for residue-pair scores at protein/protein interfaces |
| CInterface | |
| CInterfaceInfo | Keep track of the interface information |
| CResidualDipolarCouplingRigidSegments | ResidualDipolarCouplingRigidSegmentss are mainly handled by this class related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingRigidSegmentsEnergy – an energy method which triggers computations handled by this class |
| CVDW_CachedRepScreenInfo | |
| CVDW_GridEnergy | |
| CVDW_GridEnergyCreator | |
| ►Nseeded_abinitio | |
| CCAcstGenerator | |
| CCAcstGeneratorCreator | |
| CCloseFold | |
| CCloseFoldCreator | |
| CCoordinateCst | |
| CCoordinateCstCreator | |
| CDefineMovableLoops | |
| CDefineMovableLoopsCreator | |
| CGrowPeptides | |
| CGrowPeptidesCreator | |
| CSeedFoldTree | |
| CSeedFoldTreeCreator | |
| CSeedSetupMover | |
| CSeedSetupMoverCreator | |
| CSegmentHybridizer | |
| CSegmentHybridizerCreator | |
| CSwapSegment | |
| CSwapSegmentCreator | |
| ►Nsewing | |
| ►Nsampling | |
| ►Nrequirements | |
| CGlobalLengthRequirement | |
| CGlobalLengthRequirementCreator | |
| CGlobalRequirement | |
| CGlobalRequirementCreator | The Creator class is responsible for creating a particular GlobalRequirement class |
| CIntraSegmentRequirement | |
| CIntraSegmentRequirementCreator | |
| CRequirementFactory | Create Features Reporters |
| CRequirementRegistrator | This templated class will register an instance of an RequirementCreator (class T) with the RequirementFactory. It will ensure that no RequirementCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CRequirementSet | |
| CResidueRetentionRequirement | |
| CResidueRetentionRequirementCreator | |
| CSegmentDsspRequirement | |
| CSegmentDsspRequirementCreator | |
| CSegmentLengthRequirement | |
| CSegmentLengthRequirementCreator | |
| ►Nscoring | |
| CAssemblyScoreFunction | |
| CAssemblyScorer | |
| CBlosumScorer | |
| CClashScorer | |
| CInterModelMotifScorer | |
| CMotifScorer | |
| CPartnerMotifScorer | |
| CAddStartnodeFragments | |
| CAddStartnodeFragmentsCreator | |
| CAppendAssemblyMover | |
| CAppendAssemblyMoverCreator | |
| CAssembly | An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher |
| CAssemblyConstraintsMover | |
| CAssemblyConstraintsMoverCreator | |
| CAssemblyFactory | An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher |
| CAssemblyMover | |
| CBasis | |
| Cbasis_pair_equal_to | |
| Cbasis_pair_hash | |
| CContinuousAssembly | An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher |
| Ccoord_equal_to | |
| Ccoord_hash | |
| CDisembodiedAssembly | An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher |
| CEnumerateAssemblyMover | |
| CEnumerateAssemblyMoverCreator | |
| CGivenPathAssemblyMover | |
| CGivenPathAssemblyMoverCreator | |
| CGreedyAssemblyMover | |
| CGreedyAssemblyMoverCreator | |
| CHashEdge | |
| CHasher | |
| CHashResult | |
| CHashValue | |
| CModel | |
| CModelConstIterator | |
| CModelIterator | |
| CModelNode | |
| CMonteCarloAssemblyMover | |
| CMonteCarloAssemblyMoverCreator | |
| CReadNativeRotamersFile | |
| CReadNativeRotamersFileCreator | |
| CReadRepeatNativeRotamersFile | |
| CReadRepeatNativeRotamersFileCreator | |
| CRepeatAssemblyMover | |
| CRepeatAssemblyMoverCreator | |
| Csegment | |
| CSegmentGraph | |
| CSewAtom | |
| CSewGraph | |
| CSewResidue | |
| CSewSegment | |
| ►Nsic_dock | |
| ►Nscores | |
| CMotifHashRigidScore | |
| CTrisBpyScore | |
| CAtomIDHashFunction | |
| CBuriedPolarScore | |
| CCBScore | |
| CCBScoreVisitor | |
| CConstraintSetScore | |
| CCorrectionVisitor | |
| CEdgeStandScore | |
| CHelixScore | |
| CJointScore | |
| CLinkerScore | |
| CNoPoseXYX_Func | |
| CRigidScore | |
| CRose | |
| CSICFast | |
| CVec3 | |
| CXfoxmScore | |
| CxyzStripeHashPoseWithMeta | |
| ►Nsimple_filters | |
| CAbinitioBaseFilter | |
| CAlaScan | |
| CAlaScanFilterCreator | |
| CAngleToVector | |
| CAngleToVectorFilterCreator | |
| CAtomicContactFilter | Detects atomic (<4Ang) contacts between any two atoms of two residues |
| CAtomicContactFilterCreator | |
| CAtomicDistanceFilter | Detects atomic contacts between two atoms of two residues |
| CAtomicDistanceFilterCreator | |
| CAveragePathLengthFilter | |
| CAveragePathLengthFilterCreator | |
| CBatchEvaluator | |
| CBatchNrEvaluator | |
| CBuriedUnsatHbondFilter | Filters based on an upper bound # of buried unsatisfied polar residues |
| CBuriedUnsatHbondFilterCreator | |
| CCamShiftEvaluator | |
| CCamShiftEvaluatorCreator | Creator for the CamShiftEvaluatorCreator class |
| CChiWellRmsdEvaluator | |
| CChiWellRmsdEvaluatorCreator | Creator for the ChiWellRmsdEvaluatorCreator class |
| CCOFilter | |
| CConservedPosMutationFilter | |
| CConservedPosMutationFilterCreator | |
| CConstraintScoreCutoffFilter | |
| CConstraintScoreCutoffFilterCreator | |
| CConstraintScoreFilter | Filter that computes scores of constraints generated by ConstraintGenerators |
| CConstraintScoreFilterCreator | |
| CContactMapEvaluator | |
| CContactMapEvaluatorCreator | Creator for the ContactMapEvaluatorCreator class |
| CDdgFilter | |
| CDdgFilterCreator | |
| CDdGScan | |
| CDdGScanCreator | |
| CDeltaFilter | |
| CDeltaFilterCreator | |
| CDisulfideEntropyFilter | |
| CDisulfideEntropyFilterCreator | |
| CDomainInterfaceFilter | |
| CEnergyPerResidueFilter | |
| CEnergyPerResidueFilterCreator | |
| CEvaluatedTrialMover | |
| CEXCN_CalcFailed | Super-simple exception to be thrown when the SC calculator fails to compute |
| CEXCN_InitFailed | Super-simple exception to be thrown when we can't initialize the SC calculator |
| CExpiryFilter | |
| CExpiryFilterCreator | |
| CExternalEvaluator | |
| CExtraScoreEvaluatorCreator | Creator for the ExtraScoreEvaluatorCreator class |
| CFileExistFilter | |
| CFileExistFilterCreator | |
| CFileRemoveFilter | |
| CFileRemoveFilterCreator | |
| CGeometryFilter | |
| CGeometryFilterCreator | |
| CHolesFilter | |
| CHolesFilterCreator | |
| CIdManager | |
| CInterfaceBindingEnergyDensityFilter | |
| CInterfaceBindingEnergyDensityFilterCreator | |
| CInterfaceSasaFilter | |
| CInterfaceSasaFilterCreator | |
| CInterRepeatContactFilter | |
| CInterRepeatContactFilterCreator | |
| CIntraRepeatContactFilter | |
| CIntraRepeatContactFilterCreator | |
| CJScoreEvaluator | |
| CJScoreEvaluatorCreator | Creator for the JScoreEvaluatorCreator class |
| CJumpEvaluator | |
| CJumpNrEvaluator | |
| CJumpNrEvaluatorCreator | Creator for the JumpNrEvaluatorCreator class |
| CLeastNativeLike9merFilter | |
| CLeastNativeLike9merFilterCreator | |
| CLoopRmsdEvaluator | |
| CMotifScoreFilter | |
| CMotifScoreFilterCreator | |
| CMultipleSigmoids | Simply takes a list of pdbs and creates relative pose then extract sigmoids and call operator (product) |
| CMultipleSigmoidsFilterCreator | |
| CMutationsFilter | |
| CMutationsFilterCreator | |
| CNativeEvaluatorCreator | Creator for the NativeEvaluatorCreator class |
| CNeighborTypeFilter | |
| CNeighborTypeFilterCreator | |
| CNetChargeFilter | |
| CNetChargeFilterCreator | |
| Cnmer_svm_res_data | |
| CNMerPSSMEnergyFilter | |
| CNMerPSSMEnergyFilterCreator | |
| CNMerSVMEnergyFilter | |
| CNMerSVMEnergyFilterCreator | |
| CNonSequentialNeighborsFilter | |
| CNonSequentialNeighborsFilterCreator | |
| COperator | Simply take a list of filters and combine them using the operation above |
| COperatorFilterCreator | |
| CPackerNeighborGraphFilter | |
| CPackStatFilter | |
| CPackStatFilterCreator | |
| CPalesEvaluator | |
| CPalesEvaluatorCreator | Creator for the PalesEvaluatorCreator class |
| CPDDFScoreFilter | |
| CPoolEvaluatorCreator | Creator for the PoolEvaluatorCreator class |
| CPoseComment | Test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts |
| CPoseCommentFilterCreator | |
| CPoseInfoFilter | Detects atomic contacts between two atoms of two residues |
| CPoseInfoFilterCreator | |
| CPoseMetricEvaluator | |
| CPredictedBurialEvaluator | |
| CPredictedBurialFnEvaluatorCreator | Creator for the PredictedBurialFnEvaluatorCreator class |
| CQuat | |
| CRangeFilter | |
| CRangeFilterCreator | |
| CRDC_Evaluator | |
| CRdcEvaluatorCreator | Creator for the RdcEvaluatorCreator class |
| CRdcSelectEvaluatorCreator | Creator for the RdcSelectEvaluatorCreator class |
| CRdcTargetEvaluatorCreator | Creator for the RdcTargetEvaluatorCreator class |
| CRegionalConnections | |
| CRelativePoseFilter | |
| CRelativePoseFilterCreator | |
| CRepeatParameterFilter | |
| CRepeatParameterFilterCreator | |
| CReportFilter | |
| CReportFilterCreator | |
| CResidueBurialFilter | |
| CResidueBurialFilterCreator | |
| CResidueCountFilter | |
| CResidueCountFilterCreator | |
| CResidueDepthCalculator | |
| CResidueDepthData | |
| CResidueDepthFilter | |
| CResidueDepthFilterCreator | |
| CResidueDepthFrag | |
| CResidueDistanceFilter | |
| CResidueDistanceFilterCreator | |
| CResidueIEFilter | |
| CResidueIEFilterCreator | |
| CResidueSelectionDistanceFilter | |
| CResidueSelectionDistanceFilterCreator | |
| CResidueSetChainEnergyFilter | |
| CResidueSetChainEnergyFilterCreator | |
| CResiduesInInterfaceFilter | |
| CResiduesInInterfaceFilterCreator | |
| CRGFilter | |
| CRmsdEvaluator | |
| CRmsdEvaluatorCreator | Creator for the RmsdEvaluatorCreator class |
| CRmsdTargetEvaluatorCreator | Creator for the RmsdTargetEvaluatorCreator class |
| CRotamerBoltzmannWeight | |
| CRotamerBoltzmannWeight2 | Next-generation RotamerBoltzmannWeight filter |
| CRotamerBoltzmannWeight2Creator | |
| CRotamerBoltzmannWeightFilterCreator | |
| CSavePoseConstraintToFileFilter | Detects atomic contacts between two atoms of two residues |
| CSavePoseConstraintToFileFilterCreator | |
| CSaveResfileToDiskFilter | |
| CSaveResfileToDiskFilterCreator | |
| CSAXSScoreFilter | |
| CScoreCutoffFilter | |
| CScoreCutoffFilterCreator | |
| CScoreEvaluator | That rewrites the whole pss struct all previous entries will be lost... probably not what one wants.. |
| CScoreTypeFilter | |
| CScoreTypeFilterCreator | |
| CSelectGdtEvaluator | |
| CSelectMaxsubEvaluator | |
| CSelectRDC_Evaluator | |
| CSelectRmsdEvaluator | |
| CShapeComplementarityFilter | |
| CShapeComplementarityFilterCreator | |
| CSheetFilter | |
| CSidechainRmsdFilter | |
| CSidechainRmsdFilterCreator | |
| CSigmoid | Transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset |
| CSigmoidFilterCreator | |
| CSimpleHbondsToAtomFilter | Simple filter for detercting Hbonds to atom with energy < energy cutoff |
| CSimpleHbondsToAtomFilterCreator | |
| CSSElementBisectddGFilter | |
| CSSElementBisectddGFilterCreator | |
| CSSElementMotifContactFilter | |
| CSSElementMotifContactFilterCreator | |
| CSSMotifFinder | |
| CSSMotifFinderFilterCreator | |
| CStemFinder | |
| CStemFinderFilterCreator | |
| CStructuralSimilarityEvaluator | |
| CStructureSimilarityEvaluatorCreator | Creator for the StructureSimilarityEvaluatorCreator class |
| CSymmetricMotifFilter | |
| CSymmetricMotifFilterCreator | |
| CSymmetricRmsdEvaluator | |
| CTaskAwareSASAFilter | |
| CTaskAwareSASAFilterCreator | |
| CTaskAwareScoreTypeFilter | |
| CTaskAwareScoreTypeFilterCreator | |
| CTerminusDistanceFilter | |
| CTerminusDistanceFilterCreator | |
| CTotalSasaFilter | |
| CTotalSasaFilterCreator | |
| CTruncatedScoreEvaluator | |
| ►Nsimple_moves | |
| ►Na3b_hbs | |
| CA3BHbsPatcher | |
| ►Nasym_fold_and_dock | |
| CAsymFoldandDockMoveRbJumpMover | |
| CAsymFoldandDockRbTrialMover | |
| ►Nbb_sampler | |
| CBBDihedralSampler | This class functions to hold, access, sample on, and set independent and dependent dihedral data. It is an abstract base class for particular types of data. It should eventually be moved out of here |
| CBBDihedralSampler2D | |
| CBBDihedralSampler3D | |
| CBBDihedralSamplerBase | This class functions to hold, access, sample on, and set independent and dependent dihedral data. It is an abstract base class for particular types of data |
| CBBDihedralSamplerND | |
| CSmallBBSampler | A bb sampler that samples within a range of a starting angle. Similar to small mover. Samples an angle +/- the current angle. If angle max is not set, will sample any angle |
| CSugarBBSampler | Sample dihdrals using sugar bb data |
| ►Nbin_transitions | |
| CInitializeByBins | A mover to set mainchain torsions by bin transition probabilities |
| CInitializeByBinsCreator | |
| CPerturbByBins | A mover to set mainchain torsions by bin transition probabilities |
| CPerturbByBinsCreator | |
| ►Nchiral | |
| CChiralMover | |
| ►Nhbs | |
| CHbsPatcher | |
| ►Noop | |
| COopDPuckMinusMover | |
| COopDPuckPlusMover | |
| COopMover | |
| COopPatcher | |
| COopPuckMinusMover | |
| COopPuckPlusMover | |
| COopRandomPuckMover | |
| COopRandomSmallMover | |
| ►Nrational_mc | |
| CRationalMonteCarlo | |
| ►Nsidechain_moves | |
| CJumpRotamerSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CJumpRotamerSidechainMoverCreator | |
| CPerturbChiSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CPerturbChiSidechainMoverCreator | |
| CPerturbRotamerSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CPerturbRotamerSidechainMoverCreator | |
| CSetChiMover | A mover to change one chi angle |
| CSetChiMoverCreator | |
| CSidechainMCMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CSidechainMCMoverCreator | |
| CSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CSidechainMoverBase | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CSidechainMoverCreator | |
| ►Nsymmetry | |
| CDetectSymmetry | |
| CDetectSymmetryMoverCreator | |
| CExtractAsymmetricPoseMover | |
| CExtractAsymmetricPoseMoverCreator | |
| CExtractAsymmetricUnitMover | |
| CExtractAsymmetricUnitMoverCreator | |
| CFaSymDockingSlideTogether | Slides docking partners together by monitoring fa_rep |
| CNCSResMapping | |
| COrderedSequentialSymmetrySlider | |
| CRandomSymmetrySlider | |
| CSequentialSymmetrySlider | |
| CSetupForSymmetryMover | |
| CSetupForSymmetryMoverCreator | |
| CSetupNCSMover | |
| CSetupNCSMoverCreator | |
| CSymDockingInitialPerturbation | |
| CSymDockingSlideIntoContact | Contrary to the name, slides things apart first, then together |
| CSymEnergyCutRotamerTrialsMover | |
| CSymmetricRMSMover | |
| CSymmetrySlider | |
| CSymMinMover | |
| CSymMinMoverCreator | |
| CSymPackRotamersMover | |
| CSymPackRotamersMoverCreator | |
| CSymRotamerTrialsMover | |
| CSymRotamerTrialsMoverCreator | |
| CSymShakeStructureMover | |
| CTaskAwareSymMinMover | |
| CTaskAwareSymMinMoverCreator | |
| ►Ntriazolamer | |
| CTriazolamerMover | |
| CTriazolamerRandomSmallMover | |
| CAcceptedScores | Represents a set of filter scores that have been accepted |
| CAddCavitiesMover | |
| CAddChainMover | |
| CAddChainMoverCreator | |
| CAddConstraintsToCurrentConformationMover | |
| CAddConstraintsToCurrentConformationMoverCreator | |
| CAddJobPairData | Add an arbitrary piece of data to the current Job, which will be output in the silent file, database, etc. This is useful for adding metadata to keep track of data generated using multiple experimental conditions. Currently ONLY RosettaScript interface supported |
| CAddJobPairDataCreator | |
| CAlignChainMover | Align a chain in the working pose to a chain. CA superposition |
| CAlignChainMoverCreator | |
| CBackboneMover | BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.) |
| CBBConRotMover | |
| CBBDihedralSamplerMover | Mover interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them |
| CBBDihedralSamplerMoverCreator | |
| CBBG8T3AMover | Particular gaussian mover from the original paper |
| CBBGaussianMover | Basic class for implementing Gaussian Perturbation of bb |
| CBBGaussianMoverCreator | |
| CBoltzmannRotamerMover | |
| CBoltzmannRotamerMoverCreator | |
| CChainGroupDiscriminator | |
| CChainSplitMover | ChainSplitMover splits a pose into two chains given a cutpoint. This may be necessary for evaluating a domain interface using classes such as the InterfaceAnalyzerMover |
| CChangeAndResetFoldTreeMover | Basic mover used primarily for setting up atomic protocols, especially in generator functions |
| CChangeAndResetFoldTreeMoverCreator | |
| CClassicFragmentMover | A FragmentMover that applies uniform sampling of fragments |
| CClearConstraintsMover | |
| CClearConstraintsMoverCreator | |
| CCombinePoseMover | |
| CConsensusDesignMover | This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed |
| CConsensusDesignMoverCreator | |
| CConstrainToIdealMover | |
| CConstraintSetMover | |
| CConstraintSetMoverCreator | |
| CContingentAcceptMover | |
| CContingentAcceptMoverCreator | |
| CConvertRealToVirtualMover | Mover for switching a residue type to all VIRTUAL. A VIRTUAL Residue is one that is not scored or output |
| CConvertRealToVirtualMoverCreator | |
| CConvertVirtualToRealMover | Mover for switching from VIRTUAL residues to REAL residues. A VIRTUAL residue is one that is not scored or output |
| CConvertVirtualToRealMoverCreator | |
| CCopyDofMover | |
| CCopyRotamerMover | A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another |
| CCopyRotamerMoverCreator | |
| CCoupledMover | JAB - This mover has NO documentation. If you know what this mover does and how it works, please put the info HERE! |
| CCoupledMoverCreator | |
| CCstInfoMover | A Mover to output information about constraints |
| CCstInfoMoverCreator | |
| CCutChainMover | Simple mover that sperates Fv from Fl into two seperate chains |
| CCutChainMoverCreator | |
| CCyclizationMover | |
| CddG | |
| CddGCreator | |
| CDeleteChainMover | |
| CDeleteChainMoverCreator | |
| CDeleteChainsMover | Delete a chain from a Pose, or a set of chains |
| CDeleteChainsMoverCreator | |
| CDesignRepackMover | Pure virtual base class for movers which redesign and repack the interface |
| CDisulfideInsertionMover | |
| CDisulfideInsertionMoverCreator | |
| CDME_FilterMover | |
| CDOFHistogramRecorder | |
| CDumpPdb | What you think this can now be assimilated into DumpPdbMover |
| CDumpPdbCreator | |
| CEnergyCutRotamerTrialsMinMover | Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant |
| CEnergyCutRotamerTrialsMover | |
| CEvolutionaryDynamicsMover | |
| CEvolutionaryDynamicsMoverCreator | |
| CExtendedPoseMover | |
| CExtendedPoseMoverCreator | |
| CFavorSequenceProfile | |
| CFavorSequenceProfileCreator | |
| CFavorSymmetricSequence | |
| CFavorSymmetricSequenceCreator | |
| CFindConsensusSequence | |
| CFindConsensusSequenceCreator | |
| CForceDisulfidesMover | Simple mover that fixes disulfides according to a defined list and then simultaneously repacks within 6A shells around each affected cystein residue |
| CForceDisulfidesMoverCreator | |
| CFragmentCost | |
| CFragmentMover | Abstract base class for FragmentMovers |
| CGenericMonteCarloMover | |
| CGenericMonteCarloMoverCreator | |
| CGenericSimulatedAnnealer | GenericSimulatedAnnealer mover for performing simulated annealing trajectories |
| CGenericSimulatedAnnealerCreator | |
| CGreenPacker | |
| CGroupDiscriminator | Interface class used to break a pose down into a set of component "groups" where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings |
| CGunnCost | |
| CGunnTuple | |
| CHit | |
| CIonizableResidue | |
| Cless_then_match_rmsd | |
| CLoadPDBMover | |
| CLoadPDBMoverCreator | |
| CLoadUnboundRotMover | |
| CLoadUnboundRotMoverCreator | |
| ►CLoggedFragmentMover | |
| CItem | |
| CMakePolyXMover | |
| CMakePolyXMoverCreator | |
| CMembraneTopology | A mover to change one torsion angle |
| CMembraneTopologyCreator | |
| ►CMergePDBMover | |
| COverlap | |
| CMergePDBMoverCreator | |
| CMinimalRotamer | |
| CMinMover | A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set |
| CMinMoverCreator | |
| CMinPackMover | Mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing |
| CMinPackMoverCreator | |
| CMissingDensityToJumpMover | |
| CModifyVariantTypeMover | Adds variant types to selected residues |
| CModifyVariantTypeMoverCreator | |
| CMonteCarloRecover | |
| CMonteCarloRecoverCreator | |
| CMonteCarloReset | |
| CMonteCarloResetCreator | |
| CMonteCarloTest | |
| CMonteCarloTestCreator | |
| CMSDMover | |
| CMSDMoverCreator | |
| CMutateResidue | A mover to mutate a single residue |
| CMutateResidueCreator | |
| CPackRotamersMover | A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing |
| CPackRotamersMoverCreator | |
| CPackRotamersMoverLazy | Mover that packs the side-chains using a rotamer library in a lazy fashion |
| CPackRotamersMoverLazyCreator | |
| CPDBReloadMover | |
| CPDBReloadMoverCreator | |
| CPeptideStapleMover | |
| CPeriodicBoxMover | |
| CPeriodicBoxMoverCreator | |
| CPertMinMover | Random perturbation, followed by minimization |
| CPertMinMoverCreator | |
| CProlineFixMover | |
| CPSSM2BfactorMover | |
| CPSSM2BfactorMoverCreator | |
| CRandomOmegaFlipMover | |
| CRandomOmegaFlipMoverCreator | |
| CRandomTorsionMover | |
| CRandomTorsionMoverCreator | |
| CRepackSidechainsMover | A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains() |
| CRepackSidechainsMoverCreator | |
| CRepeatPropagationMover | |
| CRepeatPropagationMoverCreator | |
| CReportEffectivePKA | Scale density map intensities to match a pose's |
| CReportEffectivePKACreator | |
| CRepulsiveOnlyMover | This mover replace designated residues with glycines, and then assigns a "REPLONLY" residue type to those glycines. Those "REPLONLY" residues will make only repulsive contributions to the overall energy |
| CResetBaselineMover | |
| CResetBaselineMoverCreator | |
| CResetFoldTree | |
| CResetFoldTreeCreator | |
| CResidueTypeConstraintMover | |
| CResidueTypeConstraintMoverCreator | |
| CResTypeFragmentMover | |
| CReturnSidechainMover | |
| CRingConformationMover | |
| CRingConformationMoverCreator | MoverCreator allowing the MoverFactory to create a RingConformationMover |
| CRotamerizeMover | Mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set |
| CRotamerTrialsMinMover | |
| CRotamerTrialsMinMoverCreator | |
| CRotamerTrialsMover | |
| CRotamerTrialsMoverCreator | |
| CSaneMinMover | |
| CSaneMinMoverCreator | |
| CScoreMover | |
| CScoreMoverCreator | |
| CSequenceProfileMover | |
| CSequenceProfileMoverCreator | |
| CSetReturningPackRotamersMover | |
| CSetTorsion | A mover to change one torsion angle |
| CSetTorsionCreator | |
| CShakeStructureMover | |
| CShearMover | A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified |
| CShearMoverCreator | |
| CShortBackrubMover | |
| CShortBackrubMoverCreator | |
| CSimpleThreadingMover | This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling |
| CSimpleThreadingMoverCreator | |
| CSmallMover | A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified |
| CSmallMoverCreator | |
| CSmoothFragmentMover | |
| CSmoothSymmetricFragmentMover | A SymmetricFragmentMover that applies uniform sampling of fragments |
| CStorePoseSnapshot | A mover to store current residue indices in a map that will be updated as residues are added or deleted, permitting residue indices from the current state to be used to set up movers applied in the future |
| CStorePoseSnapshotCreator | |
| CStructProfileMover | |
| CStructProfileMoverCreator | |
| CSuperimposeMover | Superimpose pose onto reference pose. Default CA only. All residues. Optionally set to superimpose regions or backbone only (N, C, CA, O) |
| CSuperimposeMoverCreator | |
| CSwitchChainOrderMover | |
| CSwitchChainOrderMoverCreator | |
| CSwitchResidueTypeSetMover | A mover that switches a pose between residue type sets (e.g. centroid and fullatom) |
| CSwitchResidueTypeSetMoverCreator | |
| CSymmetricFragmentMover | A SymmetricFragmentMover that applies uniform sampling of fragments |
| CTailsScoreMover | |
| CTaskAwareMinMover | |
| CTaskAwareMinMoverCreator | |
| CThermodynamicData | Structure that stores data during simulation |
| CTorsionDOFMover | TODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code) |
| CTorsionSetMover | |
| CTumble | |
| CTumbleCreator | |
| CUniformRotationMover | Uniform Rotation Mover |
| CUniformTranslationMover | Uniform Translation Mover |
| CUserDefinedGroupDiscriminator | |
| CVirtualRootMover | |
| CVirtualRootMoverCreator | |
| CWobbleMover | A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: -—lfff bbb-— f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl— the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment() |
| ►Nsparta | |
| CANN | |
| CChemicalShiftEvaluator | |
| CChemicalShiftEvaluatorCreator | Creator for the ChemicalShiftsEvaluatorCreator class |
| CGDB | |
| CPDB | |
| CPDB_Entry | |
| CRingData | |
| ►CSparta | |
| CSpartaLib | { most of the original SPARTA class goes into SpartaLib – to be reused between different evaluators.. |
| ►Nss_prediction | |
| CSS_predictor | |
| ►Nstar | |
| CExtender | |
| CStarAbinitio | |
| ►Nstepwise | |
| ►Nlegacy | |
| ►Nmodeler | |
| ►Nprotein | |
| CStepWiseProteinMinimizer | |
| CStepWiseProteinPoseSetup | |
| ►Nrna | |
| CCluster_Member | |
| CRNA_AnalyticLoopCloser | The RNA de novo structure modeling protocol |
| CSlicedPoseWorkingParameters | |
| CStepWiseRNA_Clusterer | |
| CStepWiseRNA_PoseSelection | |
| CStepWiseRNA_PoseSetup | |
| CStepWiseWorkingParametersSetup | |
| ►Nscreener | |
| CProteinAtrRepScreener | |
| CRNA_AtrRepScreener | |
| CSimplePoseSelection | |
| CSimpleRMSD_Screener | |
| ►Nmodeler | |
| ►Nalign | |
| CStepWiseClusterer | |
| CStepWiseLegacyClusterer | |
| CStepWiseLegacyClustererSilentBased | |
| CStepWisePoseAligner | |
| ►Noptions | |
| CStepWiseBasicModelerOptions | |
| CStepWiseModelerOptions | |
| CStepWiseProteinModelerOptions | |
| CStepWiseRNA_ModelerOptions | |
| ►Npacker | |
| CSideChainCopier | |
| CStepWiseMasterPacker | |
| CStepWisePacker | |
| ►Npolar_hydrogens | |
| CPolarHydrogenPacker | |
| ►Nprecomputed | |
| CPrecomputedLibraryMover | |
| ►Nprotein | |
| ►Nchecker | |
| CProteinAtrRepChecker | |
| ►Nloop_close | |
| CStepWiseProteinCCD_Closer | |
| CStepWiseProteinCCD_MultiPoseCloser | |
| CStepWiseProteinKIC_LoopBridger | |
| CInputStreamWithResidueInfo | |
| CMainChainTorsionSet | |
| CStepWiseProteinBackboneSampler | |
| ►Nrna | |
| ►Nbulge | |
| CBulgeApplyMover | |
| CBulgeUnApplyMover | |
| ►Nchecker | |
| CRNA_AtrRepChecker | |
| CRNA_BaseCentroidChecker | |
| CRNA_ChainClosableGeometryChecker | |
| CRNA_ChainClosureChecker | |
| CRNA_VDW_BinChecker | |
| ►Nhelix | |
| CRNA_HelixAssembler | The RNA de novo structure modeling protocol |
| ►No2prime | |
| CO2PrimePacker | |
| ►Nphosphate | |
| CMultiPhosphateSampler | |
| CPhosphateMove | |
| CPhosphateMover | |
| ►Nrigid_body | |
| CBaseBin | |
| Ccompare_base_bin | |
| Ccompare_int_pair | |
| ►Nsugar | |
| CSugarInstantiateMover | |
| CSugarModeling | |
| CSugarVirtualizeMover | |
| CVirtualSugarJustInTimeInstantiator | |
| CVirtualSugarSampler | |
| CVirtualSugarSamplerFromStringList | |
| CCombine_Tags_Info | |
| CFilterer_Count | |
| CInternalWorkingResidueParameter | |
| CJump_point | |
| Coutput_data_struct | |
| CResidue_info | |
| CStepWiseRNA_CombineLongLoopFilterer | |
| CStepWiseRNA_CountStruct | |
| CTorsion_Info | |
| ►Nworking_parameters | |
| CStepWiseBasicWorkingParameters | |
| CStepWiseWorkingParameters | |
| CStepWiseConnectionSampler | |
| CStepWiseMinimizer | |
| CStepWiseModeler | |
| ►Nmonte_carlo | |
| ►Nmover | |
| ►Noptions | |
| CStepWiseMoveSelectorOptions | |
| CAddMover | |
| CAddOrDeleteMover | |
| CAttachment | |
| CDeleteMover | |
| CFromScratchMover | |
| CResampleMover | |
| CStepWiseMasterMover | |
| CStepWiseMove | |
| CStepWiseMoveSelector | |
| CTransientCutpointHandler | |
| CVaryLoopLengthMover | In stepwise design, vary desired loop lengths by updating FullModelParameters |
| ►Noptions | |
| CStepWiseMonteCarloOptions | |
| ►Nrna | |
| CRNA_AddDeleteMonteCarlo | |
| CRNA_O2PrimeMover | |
| CRNA_TorsionMover | |
| ►Nsubmotif | |
| CSubMotifLibrary | |
| CStepWiseMonteCarlo | |
| ►Noptions | |
| CStepWiseBasicOptions | |
| ►Nsampler | |
| ►Ncopy_dofs | |
| CCopyDofStepWiseSampler | |
| CResidueAlternativeSet | |
| CResidueAlternativeStepWiseSampler | |
| CResidueAlternativeStepWiseSamplerComb | |
| CResidueListStepWiseSampler | |
| ►Ninput_streams | |
| CInputStreamStepWiseSampler | |
| ►Njump | |
| CJumpStepWiseSampler | |
| ►Nprotein | |
| CProteinBetaAntiParallelStepWiseSampler | |
| CProteinFragmentStepWiseSampler | |
| CProteinMainChainStepWiseSampler | |
| ►Nrigid_body | |
| CEulerAngles | |
| CRigidBodyStepWiseSampler | |
| CRigidBodyStepWiseSamplerValueRange | |
| CRigidBodyStepWiseSamplerWithResidueAlternatives | |
| CRigidBodyStepWiseSamplerWithResidueList | |
| ►Nrna | |
| CRNA_ChiStepWiseSampler | |
| CRNA_KIC_Sampler | |
| CRNA_KinematicCloser | The RNA de novo structure modeling protocol |
| CRNA_NucleosideStepWiseSampler | |
| CRNA_SugarStepWiseSampler | |
| CRNA_SuiteStepWiseSampler | |
| ►Nscreener | |
| CRNA_TorsionScreener | |
| CStepWiseSampler | |
| CStepWiseSamplerComb | |
| CStepWiseSamplerOneTorsion | |
| CStepWiseSamplerOneValue | |
| CStepWiseSamplerOneValueComb | |
| CStepWiseSamplerSized | |
| CStepWiseSamplerSizedAny | |
| CStepWiseSamplerSizedComb | |
| ►Nscreener | |
| CAlignRMSD_Screener | |
| CAnchorSugarScreener | |
| CBaseBinMapUpdater | |
| CBaseCentroidScreener | |
| CBulgeApplier | |
| CCentroidDistanceScreener | |
| CFastForwardToNextResidueAlternative | |
| CFastForwardToNextRigidBody | |
| CIntegrationTestBreaker | |
| CO2PrimeScreener | |
| CPackScreener | |
| CPartitionContactScreener | |
| CPhosphateScreener | |
| CPoseSelectionScreener | |
| CProteinCCD_ClosureScreener | |
| CResidueContactScreener | |
| CRNA_ChainClosableGeometryResidueBasedScreener | |
| CRNA_ChainClosableGeometryScreener | |
| CRNA_ChainClosableGeometryStubBasedScreener | |
| CRNA_ChainClosureScreener | |
| CSampleApplier | |
| CScorer | |
| CStepWiseResiduePairScreener | |
| CStepWiseScreener | |
| CStubApplier | |
| CStubDistanceScreener | |
| CSugarInstantiator | |
| CTagDefinition | |
| CVDW_BinScreener | |
| ►Nsetup | |
| CStepWiseCSA_JobDistributor | |
| CStepWiseJobDistributor | |
| CStepWiseMonteCarloJobDistributor | |
| CStepWiseSampleAndScreen | |
| ►Nstruct_fragment | |
| CStructFragmentMover | |
| CStructFragmentMoverCreator | RosettaScripts factory for StructFragmentMover |
| ►Nsurface_docking | |
| CCentroidRelaxMover | |
| CFullatomRelaxMover | |
| CSurfaceDockingProtocol | |
| CSurfaceOrientMover | |
| CSurfaceParameters | |
| CSurfaceVectorFallbackConfiguration | |
| CSurfaceVectorFallbackConfigurationCreator | |
| CSurfaceVectorLoader | SurfaceVectorLoader constructs a SurfaceParameters instance from data provided by the resource manager |
| CSurfaceVectorLoaderCreator | |
| CSurfaceVectorOptions | |
| CSurfaceVectorOptionsCreator | |
| ►Nsymmetric_docking | |
| ►Nmembrane | |
| CMPSymDockMover | |
| CMPSymDockMoverCreator | Mover Creator |
| CSymDockBaseProtocol | |
| CSymDockingHiRes | |
| CSymDockingLowRes | |
| CSymDockProtocol | Main Symmetric Docking protocol class |
| CSymDockProtocolCreator | |
| CSymFoldandDockMoveRbJumpMover | |
| CSymFoldandDockMoveRbJumpMoverCreator | |
| CSymFoldandDockRbTrialMover | |
| CSymFoldandDockRbTrialMoverCreator | |
| CSymFoldandDockSlideTrialMover | |
| CSymFoldandDockSlideTrialMoverCreator | |
| CSymInterfaceSidechainMinMover | |
| CSymRestrictTaskForDocking | |
| CSymSidechainMinMover | |
| ►Ntoolbox | |
| ►Nmatch_enzdes_util | |
| CAlignPoseToInvrotTreeMover | Small mover that takes an invrot tree |
| CAllowedSeqposForGeomCst | Simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too |
| CCovalentConnectionReplaceInfo | Helper class to allow for removal of covalent constraints |
| CCstResInteractions | |
| CEnzConstraintIO | |
| CEnzConstraintParameters | Class that holds all the parameters for one specific constraint |
| CEnzCstTemplateRes | Helper class for class EnzConstraintParameters, gathers information |
| CEnzCstTemplateResAtoms | Helper class for EnzCstTemplateRes, holds atom ids corresponding |
| CEnzCstTemplateResCache | |
| CEnzdesCacheableObserver | |
| CEnzdesCstCache | Simple class to store the pose specific enzdes constraint information in the actual pose |
| CEnzdesCstParamCache | |
| CEnzdesLoopInfo | |
| CEnzdesLoopsFile | Class to process an enzdes loops file |
| CEnzdesSeqRecoveryCache | |
| CExternalGeomSampler | The external geom sampler is a class that manages the data necessary to construct the coordinates of the three atoms in the downstream partner |
| CGeomSampleInfo | Class that stores information of one geometric parameter line of the .cst file i.e. angleA or torsionB |
| CInvrotCollector | @ brief helper class for collecting all different definitions of invrots from a tree |
| CInvrotTarget | 'root' target against which the inverse rotamers are built abstract base class to allow for invrots being built against any sort of entity |
| CInvrotTree | |
| CInvrotTreeNode | |
| CInvrotTreeNodeBase | Abstract base class for an inverse rotamer tree node. Exists so that the target node (InvrotTreeTarget) and the different geom cst nodes (InvrotTreeNode) have a common base class. This is necessary so that a node can point at its parent node in a tree without having to worry about whether that is a target or a regular node |
| CLigandConformer | |
| CMatchConstraintFileInfo | |
| CMatchConstraintFileInfoList | Simple container class to contain several MatchConstraintFileInfo instances. this can also query the MatchConstraintFileInfos for common upstream restypes and put all their geomsamples into one list |
| CResInteractions | |
| CSingleResidueInvrotTarget | |
| CTheozymeInvrotTree | This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile. It gets complicated when ambiguous interactions are specified and other residues are interacting (possibly in ambiguous fashion) with these ambiguous residues.. |
| ►Npose_metric_calculators | |
| CBuriedUnsatisfiedPolarsCalculator | |
| CCatPiCalculator | |
| CChargeCalculator | |
| CClashCountCalculator | |
| CDecomposeAndReweightEnergiesCalculator | |
| CEmptyVertexData | |
| CEnergiesData | |
| CFragQualCalculator | |
| CHPatchCalculator | |
| CInterGroupNeighborsCalculator | |
| CMetricValueGetter | |
| CNeighborhoodByDistanceCalculator | |
| CNeighborsByDistanceCalculator | |
| CNonlocalContactsCalculator | |
| CNumberHBondsCalculator | |
| CPackstatCalculator | |
| CPiPiCalculator | |
| CResidueDecompositionByChainCalculator | |
| CResidueDecompositionCalculator | |
| CRotamerBoltzCalculator | |
| CRotamerRecovery | |
| CSaltBridgeCalculator | |
| CSemiExplicitWaterUnsatisfiedPolarsCalculator | |
| CSequenceComparison | |
| CSHOBuriedUnsatisfiedPolarsCalculator | |
| CSurfaceCalculator | |
| ►Nrotamer_set_operations | |
| CAddGood2BPairEnergyRotamers | Implementation of rosetta 2.x style rotamer explosion builds a whole bunch of extra rotamers, but only adds them to the set if they score better than a cutoff with a given set of target residues |
| CRigidBodyMoveBaseRSO | |
| CRigidBodyMoveRSO | |
| CSpecialRotamerRSO | |
| ►Ntask_operations | |
| CAlignedThreadOperation | |
| CAlignedThreadOperationCreator | |
| CConservativeDesignOperation | A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations |
| CCrystalContactsOperation | |
| CCrystalContactsOperationCreator | |
| CDatabaseThread | |
| CDatabaseThreadCreator | |
| CDesignAroundOperation | |
| CDesignAroundOperationCreator | |
| CDockingNoRepack1 | |
| CDockingNoRepack2 | |
| CDsspDesignOperation | TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure |
| CDsspDesignOperationCreator | |
| CImportUnboundRotamersOperation | |
| CImportUnboundRotamersOperationCreator | |
| CInteractingRotamerExplosion | : taskop to oversample rotamers that make good interactions with a (set of) specified target residue(s) similar to Rosetta 2.x rotamer explosion |
| CInteractingRotamerExplosionCreator | |
| CInterfaceTaskOperation | |
| CJointSequenceOperation | |
| CJointSequenceOperationCreator | |
| CLimitAromaChi2_RotamerSetOperation | |
| CLimitAromaChi2Operation | |
| CLimitAromaChi2OperationCreator | |
| CLinkResidues | |
| CLinkResiduesCreator | |
| CModifyAnnealer | |
| CModifyAnnealerCreator | |
| CMutationSetDesignOperation | Sample a set of mutations each time packer is generated. A MutationSet is a simple map of resnum:aa. Each apply will sample a set either at random, or with a set of weights |
| CPreventChainFromRepackingOperation | |
| CPreventChainFromRepackingOperationCreator | |
| CPreventResiduesFromRepackingOperation | |
| CPreventResiduesFromRepackingOperationCreator | |
| CProteinCore | |
| CProteinCoreFilterCreator | |
| CProteinInterfaceDesignOperation | |
| CProteinInterfaceDesignOperationCreator | |
| CReadResfileFromDB | |
| CReadResfileFromDBCreator | |
| CResidueProbDesignOperation | A TaskOperation that allows amino acids at designable positions through a set of aa probabilities (aa profile) |
| CRestrictByCalculatorsOperation | |
| CRestrictByCalculatorsOperationCreator | |
| CRestrictChainToRepackingOperation | |
| CRestrictChainToRepackingOperationCreator | |
| CRestrictConservedLowDdgOperation | Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking |
| CRestrictConservedLowDdgOperationCreator | |
| CRestrictIdentitiesAtAlignedPositionsOperation | |
| CRestrictIdentitiesAtAlignedPositionsOperationCreator | |
| CRestrictIdentitiesOperation | |
| CRestrictIdentitiesOperationCreator | |
| CRestrictInterGroupVectorOperation | |
| CRestrictInterGroupVectorOperationCreator | |
| CRestrictNativeResiduesOperation | |
| CRestrictNativeResiduesOperationCreator | |
| CRestrictNonSurfaceToRepackingOperation | |
| CRestrictNonSurfaceToRepackingOperationCreator | |
| CRestrictOperationsBase | |
| CRestrictResiduesToRepackingOperation | |
| CRestrictResiduesToRepackingOperationCreator | |
| CRestrictToAlignedSegmentsOperation | |
| CRestrictToAlignedSegmentsOperationCreator | |
| CRestrictToCDRH3Loop | |
| CRestrictToCDRH3LoopCreator | |
| CRestrictToInterface | |
| CRestrictToInterfaceCreator | |
| CRestrictToInterfaceOperation | |
| CRestrictToInterfaceOperationCreator | |
| CRestrictToInterfaceVectorOperation | |
| CRestrictToInterfaceVectorOperationCreator | |
| CRestrictToLoops | |
| CRestrictToLoopsAndNeighbors | This class allows the selection for packing (and possibly design) of residues contained in a Loops object as well as the neighbors within a specified cutoff distance, with the default and maximum cutoff at 10.0 A |
| CRestrictToLoopsAndNeighborsCreator | |
| CRestrictToLoopsCreator | |
| CRestrictToMoveMapChiOperation | A TaskOperation that accepts a movemap and restricts chi that are false to either packing or design. Does not turn anything on, just like the rest of the RestrictTo operations |
| CRestrictToNeighborhoodOperation | |
| CRestrictToNeighborhoodOperationCreator | |
| CRestrictToTerminiOperation | |
| CRestrictToTerminiOperationCreator | |
| CRetrieveStoredTaskOperation | |
| CRetrieveStoredTaskOperationCreator | |
| CSelectByDeltaScoreOperation | |
| CSelectByDeltaScoreOperationCreator | |
| CSelectByDensityFitOperation | |
| CSelectByDensityFitOperationCreator | |
| CSelectBySASAOperation | |
| CSelectBySASAOperationCreator | |
| CSelectResiduesWithinChainOperation | |
| CSelectResiduesWithinChainOperationCreator | |
| CSeqprofConsensusOperation | |
| CSeqprofConsensusOperationCreator | |
| CSetIGTypeOperation | |
| CSetIGTypeOperationCreator | |
| CSTMStoredTask | |
| CStoreCombinedStoredTasksMover | Mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls |
| CStoreCombinedStoredTasksMoverCreator | |
| CStoreCompoundTaskMover | |
| CStoreCompoundTaskMoverCreator | |
| CStoreTaskMover | Mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls |
| CStoreTaskMoverCreator | |
| CThreadSequenceOperation | |
| CThreadSequenceOperationCreator | |
| CAtomID_Mapper | |
| CAtomLevelDomainMap | |
| CCalcInterNeighborGroup | |
| CClusterBase | |
| CClusterOptions | |
| CClusterPhilStyle | |
| CCovalentResidueNetwork | Creates networks based on covalent connections between residues |
| CDecoySetEvaluation | |
| CDistanceResidueNetwork | Creates networks based on residue proximity in space |
| CDummyClass | |
| CEnergyLandscapeEvaluator | Evaluates a set of score/rms points |
| CGreedyKCenter | Greedy K-Center Clustering Algorithm |
| CIGLigandDesignEdgeUpweighter | |
| CInteratomicVarianceMatrix | |
| CKCluster | Basic class for performing a K-style Clustering algorithm |
| CKClusterData | Database of a K-style Clustering algorithm |
| CKClusterElement | |
| CKMedoid | Typical K-Medoids Clustering Algorithm |
| CMulliganPNearEvaluator | Evaluates a set of score/rms points using Vikram's pnear method |
| CNode | |
| COP_const_iterator | Const_iterator class for SilentFileData container |
| CResidueGroupIGEdgeUpweighter | |
| CResidueNetwork | Residuenetwork base class |
| CRotamerBoltzmannWeightEvaluator | Evaluates a set of score/rms points using the RotamerBoltzmann original method |
| CSamplerPlusPlus | |
| CScoreRmsPoint | |
| CScoreRmsPoints | |
| CSF_Replica | |
| ►Ntopology_broker | |
| ►Nclaims | |
| CBBClaim | |
| CCutClaim | |
| CDofClaim | |
| CJumpClaim | |
| CLegacyRootClaim | |
| CSequenceClaim | |
| CSymmetryClaim | |
| ►Nweights | |
| CAbinitioMoverWeight | |
| CConstAbinitioMoverWeight | |
| CLargeFragWeight | |
| CSmallFragWeight | |
| CSmoothFragWeight | |
| CAsymFoldandDockClaimer | |
| CBasicJumpClaimer | |
| CClaimerMessage | |
| CCmdLineData | |
| CConstraintClaimer | |
| CConstraintEvaluatorWrapper | |
| CConstraintEvaluatorWrapperCreator | Creator for the ConstraintsEvaluatorWrapperCreator class |
| CCoordConstraintClaimer | |
| CCutBiasClaimer | |
| CDensityScoringClaimer | |
| CDisulfJumpClaimer | Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore |
| CEXCN_FailedBroking | |
| CEXCN_FilterFailed | |
| CEXCN_Input | |
| CEXCN_TopologyBroker | |
| CEXCN_Unknown | |
| CFibrilModelingClaimer | |
| CFoldandDockClaimer | |
| CFragmentClaimer | |
| CFragmentContainer | |
| CFragmentJumpClaimer | Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore |
| CLoopFragmentClaimer | |
| CMembraneTopologyClaimer | |
| CMetalloClaimer | |
| CPcsEnergyController | |
| CPseudocontactShiftEnergyController | |
| CPseudocontactShiftEnergyController_Ts1 | |
| CPseudocontactShiftEnergyController_Ts2 | |
| CPseudocontactShiftEnergyController_Ts3 | |
| CPseudocontactShiftEnergyController_Ts4 | |
| CRigidBodyRandomTMHMover | |
| ►CRigidChunkClaimer | Defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers — here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued — in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree |
| CCM_SuggestFixResidue | |
| CJumpCalculator | Helper class – computes if we have all jupms needed to rigidify the chosen chunk and generate more jumps if needed |
| CSequenceClaimer | |
| CSequenceNumberResolver | |
| CStartStructClaimer | |
| CSuggestValueMessage | |
| CSymmetryClaimer | |
| CTemplateFragmentClaimer | Hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates |
| CTemplateJumpClaimer | Hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates |
| CTMHTopologySamplerClaimer | |
| CTopologyBroker | |
| CTopologyClaimer | |
| CTopologyClaimerFactory | A non-copyable factory for instantiating TopologyClaimers by name. Commonly used TopologyClaimers are registered in the constructor. Additional claimers can be registered after the fact using the add_type() method. APL Question: Should this be one-instance-per-program (singleton) or one-instance-per-job? |
| ►Ntrajectory | |
| CDbTrajectoryReader | |
| ►CDbTrajectoryWriter | |
| CFrame | |
| ►Nub_e2c | |
| Cubi_e2c_modeler | |
| ►Nunfolded_state_energy_calculator | |
| CUnfoldedStateEnergyCalculatorJobDistributor | |
| CUnfoldedStateEnergyCalculatorMover | |
| CUnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor | |
| ►Nviewer | |
| CGraphicsState | |
| CSilentObserver | |
| Ctriangle | |
| CtriangleIterator | |
| ►Nvip | |
| CVIP_Mover | |
| CVIP_Report | |
| ►Nwum | |
| CDatabaseEntryWorkUnit | |
| Cfind_SilentStructOPs | This little class is a predicate for finding silent structures in say a vector of silent structures |
| CMoverList | |
| CMPI_WorkUnitManager | |
| CMPI_WorkUnitManager_Slave | |
| CSilentStructStore | |
| Csort_SilentStructOPs | |
| CWorkUnit_MoverWrapper | This WorkUnit type can encapsulate any MoverOP. When registering this WOrkunit provide it with a MoverOP and then, when executed on the slaves, this workunit will run the mover On every single input structure and return the results |
| CWorkUnit_SilentStructStore | This WorkUnit type has structures in it. Most Workunits should derive from this one rather THe the Base class |
| CWorkUnit_Wait | |
| ►CWorkUnitBase | The base class for all work units |
| CWU_Header | This structure can contain any non-dynamicly allocated data. Any simple data types can be used here, ints, real, floats, char, etc. |
| CWorkUnitList | WOrkUnitList is a store for WorkUnitCOPs. THe purpose of this class is to store all the possible WorkUnits that a protocol might need. When needed these are cloned and then used. THis class acts like a library of WorkUnit blueprints |
| CWorkUnitManager | |
| CWorkUnitQueue | |
| CWorkUnitQueue_Swapped | |
| CLoopRebuild | The loop-rebuild protocol |
| CLoopRefine | Class LoopRefine for fullatom loop refinement |
| CRBSegmentRelaxImpl | |
| ►Nupdate_ResidueType_enum_files | |
| CEnumInfo | |
| CA | |
| CA | |
| CA | |
| CA | Of residues |
| CA | |
| CAlternating | |
| CAn | |
| CAn | |
| CAtomTypeData | Hybridization and bond geometry data, which is used in Atom |
| CComputes | |
| CCrossoverBehavior | |
| CE | |
| CG | |
| CImplements | |
| CImplements | |
| CSimple | Associates fragment indices with Gunn scores |
| CTransformation | |
| CTrial | |
| CV |
1.8.7
