| ►Naaaa | |
| CA | |
| CC | |
| ►Nabinitio | |
| ►NAnchoredDesign | |
| ►Nantibody | |
| ►Napp | |
| ►Npyrosetta_toolkit | |
| ►Nmodules | |
| ►Ncalibur | |
| Ccalibur | |
| ►Ndefinitions | |
| ►Nrestype_definitions | |
| Cdefinitions | |
| ►NDesignBreakdown | |
| CDesignBreakdown | |
| CSequenceInfo | |
| CSequenceResults | |
| ►Nprettytable | |
| ►Nprettytable | |
| CPrettyTable | |
| ►Nprettytable_test | |
| CBasicTests | |
| CBreakLineTests | |
| CBuildEquivelanceTest | |
| CCityDataTest | |
| CFloatFormatBasicTests | |
| CFloatFormatTests | |
| CHrulesAllBasicTests | |
| CHrulesNoneBasicTests | |
| CHtmlOutputTests | |
| CIntegerFormatBasicTests | |
| CNoBorderBasicTests | |
| CNoHeaderBasicTests | |
| COptionOverrideTests | |
| CPresetBasicTests | |
| CSlicingTests | |
| CSortingTests | |
| ►Nprotocols | |
| ►NAnalysisProtocols | |
| CAnalysisProtocols | |
| CVIP_Wrapper | |
| ►NDesignProtocols | |
| CDesignProtocols | |
| CDesignWrapper | |
| ►NDockingProtocols | |
| CDockingProtocols | |
| CLowResWrapper | |
| ►NFloppyTailProtocol | |
| CFloppyTailProtocol | |
| ►NGraftingProtocols | |
| CGraftingProtocols | |
| CGraftMover | |
| CGraftMoverWindow | |
| ►NHighResLoopModelingProtocols | |
| CHighResLoopModelingProtocols | |
| ►NLowResLoopModelingProtocols | |
| CLowResLoopModelingProtocols | |
| ►NMinimizationProtocols | |
| CMinimizationProtocols | |
| ►NProtocolBaseClass | |
| CProtocolBaseClass | |
| ►NPythonPDB | |
| CPythonPDB | |
| ►NRegion | |
| CRegion | |
| CRegions | |
| ►NRegionalScoring | |
| CRegionalScoring | |
| ►NScoreAnalysis | |
| CScoreAnalysis | |
| ►NSQLPDB | |
| CPDB_database | |
| CSQLPDB | |
| ►NStructure | |
| CAntibody_Structure | |
| CAtom | |
| CBond | |
| CCDR | |
| Celectron | |
| CFRAMEWORK | |
| Cmolecule | |
| Cnucleus | |
| CPDB | |
| Cprotein | |
| Cprotein_info | |
| CResidue | |
| ►Ntools | |
| ►Ninterfaces | |
| CAntibodies | |
| Caround | |
| ►Npyrosetta_toolkit | |
| Cmain_window | |
| CMainTracer | |
| ►Nwindow_main | |
| ►Nframes | |
| ►NInputFrame | |
| CInputFrame | |
| ►NOutputFrame | |
| COutputFrame | |
| ►NQuickProtocolsFrame | |
| CQuickProtocolsFrame | |
| ►NSimpleAnalysisFrame | |
| CSimpleAnalysisFrame | |
| ►NIO | |
| ►NGUIInput | |
| CGUIInput | |
| ►NGUIOutput | |
| CGUIOutput | |
| ►NSessionIO | |
| CSessionIO | |
| ►Nmenu | |
| CMenus | |
| ►Nwindow_modules | |
| ►Nclean_pdb | |
| ►NFixPDBWindow | |
| CFixPDBWindow | |
| ►Ndesign | |
| ►NResfileDesignWindow | |
| CResfileDesignWindow | |
| ►Nfull_control | |
| ►NFullControlWindow | |
| CFullControlWindow | |
| ►Ninsert_bfactor | |
| ►NInsertBFactor | |
| CInsertBFactor | |
| ►Ninteractive_terminal | |
| ►Ninteractive_terminal | |
| CIPythonView | |
| CIterableIPShell | |
| CTkConsoleView | |
| ►Nligand_ncaa_ptm_manager | |
| ►Nligand_ncaa_ptm_manager | |
| Cligand_ncaa_ptm_manager | |
| CParamsProperties | |
| CPatchProperties | |
| CProperties | |
| ►Noptions_system | |
| ►NOptionSystemManager | |
| COptionSystemManager | |
| ►Nprotocol_builder | |
| ►NProtocolBuilder | |
| CMainProtocols | |
| ►Npymol_integration | |
| ►NPyMOL | |
| CAdvancedPyMOL | |
| ►Nscorefunction | |
| ►NScoreFxnControl | |
| CScoreFxnControl | |
| ►Nvicinity_options | |
| ►Nvicinity_window | |
| Cvicinityrelaxwindow | |
| ►Nsurface_docking | |
| ►Nmovers | |
| CAbinitio | |
| CCentroidRelax | |
| CFullAtomRelax | |
| ►Napps | |
| ►Npublic1 | |
| ►Nscenarios | |
| ►Narls_impl | |
| CDockingCase | |
| CDockingFile | |
| CPreformattedDescFormatter | |
| ►Nbasic | 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 |
| ►Ndatabase | |
| ►Ninsert_statement_generator | |
| CInsertGenerator | |
| CRowData | |
| CRowDataBase | |
| ►Nschema_generator | |
| CColumn | |
| CConstraint | |
| CDbBigInt | DOES NOT WORK WITH CPPDB - USE INTEGER INSTEAD /boolean data type |
| CDbDataType | |
| CDbDouble | |
| CDbInteger | |
| CDbReal | |
| CDbText | |
| CDbTextKey | |
| CDbUUID | |
| CForeignKey | |
| CGreaterThanConstraint | |
| CIndex | |
| CPrimaryKey | |
| CSchema | |
| CUniqueConstraint | |
| CDatabaseSessionLoader | |
| CDatabaseSessionLoaderCreator | |
| CDatabaseSessionOptions | |
| CDatabaseSessionOptionsCreator | |
| ►Ndatacache | |
| CBasicDataCache | A DataCache storing objects derived from basic::datacache::CacheableData |
| CCacheableData | Base class for data storable within a DataCache |
| CCacheableString | Wrapper for std::string |
| CCacheableStringFloatMap | Wrapper for std::map< std::string, float > |
| CCacheableStringMap | Wrapper for a map< string, string > |
| CConstDataMap | General-purpose store for any kind of object with the particular copy semantics of copying by value. This is effectively a map of string pairs to (constant) pointers. The first string represents the category of the object, and the second being a name for that particular object. The guarantee with the ConstDataMap is that if an object is put into the map, it may be read from, but it will not be changed underneath you. Data stored in the ConstDataMap can safely be shared between threads |
| CDataCache | Forward declaration for DataCache |
| CDataCache_CacheableData | |
| CDataMap | General-purpose store for any reference-count derived object |
| CDataMapObj | Templated class to make any data type compatible with ReferenceCounts and OPs. e.g., utility::pointer::owning_ptr< basic::datacache::DataMapObj< bool > > stop; You can then place such constructs on the basic::datacache::DataMap |
| CDiagnosticData | Wrapper for std::map<string, Real> |
| CHierarchicalDataMap | A data map designed to help create hierarchies with complicated shared data requirements |
| CWriteableCacheableData | Base class for data storable within a DataCache |
| CWriteableCacheableDataCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| CWriteableCacheableDataFactory | |
| CWriteableCacheableDataRegistrator | This templated class will register an instance of an WriteableCacheableDataCreator (class T) with the WriteableCacheableDataFactory. It will ensure that no WriteableCacheableDataCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CWriteableCacheableMap | Wrapper for a map< string, string > |
| ►Ngpu | |
| Cfloat4 | |
| CTimer | |
| ►Nmpi | |
| CDbMoverMessageListener | |
| CMessageListener | |
| CMessageListenerFactory | |
| ►Noptions | |
| ►NOptionKeys | |
| ►Nabinitio | |
| ►NAnchoredDesign | |
| ►Nantibody | |
| ►Nblivens | |
| ►Ncanonical_sampling | |
| ►Ncarbohydrates | |
| ►Ncm | |
| ►Ncmiles | |
| ►Ncorrections | |
| ►Ndna | |
| ►Ndesign | |
| ►Ndocking | |
| ►Nligand | |
| ►Nflexpack | |
| ►NFloppyTail | |
| ►Nflxbb | |
| ►Nfrags | |
| ►Nfull_model | |
| ►Nin | |
| ►Ninout | |
| ►Nlh | |
| ►Nloops | |
| ►Nmagnesium | |
| ►Nmatdes | |
| ►Nmh | |
| ►Nmistakes | |
| ►Nmp | |
| ►Nbenchmark | |
| ►Nms | |
| ►NoptE | |
| ►Nout | |
| ►Npacking | |
| ►NpH | |
| ►Npose_metrics | |
| ►Nrelax | |
| ►Nremodel | |
| ►Nrna | |
| ►Nfarna | |
| ►Nscore | |
| ►Nstepwise | |
| ►Nmonte_carlo | |
| ►Ntemplates | |
| ►Nufv | |
| ►Nresource_manager | |
| ►Nfallback_configuration | |
| CNativeFallbackConfiguration | |
| CNativeFallbackConfigurationCreator | |
| ►Nlocator | |
| CDatabaseResourceLocator | The DatabaseResourceLocator class is responsible for retreiving data from a Database so that that data can then be used to construct a Resource |
| CDatabaseResourceLocatorCreator | Creator for the DatabaseResourceLocator class |
| CFileListResourceLocator | The FileListResourceLocator concatenates a set of listed files; e.g. useful for constructing a pose from two separate PDB files |
| CFileListResourceLocatorCreator | Creator for the FileSystemResourceLocator class |
| CFileStream | FileStream is a wrapper class for a utility::io::izstream object that derives from ResourceStream |
| CFileSystemResourceLocator | The FileSystemResourceLocator is responsible for opening a file from the file system given its name (as the "locator tag" in the locate_resource_stream method ) and returning a FileStream object that wraps this file. This FileStream can then be used to construct a resource |
| CFileSystemResourceLocatorCreator | Creator for the FileSystemResourceLocator class |
| CNullResourceLocator | The NullResourceLocator is meant for cases where a resource can be created without reading from an input file. It goes through the motions of returning a ResourceStream (an empty NullStream) as is required of all ResourceLocators, but the stream that it creates will not be used |
| CNullResourceLocatorCreator | Creator for the NullResourceLocator class |
| CNullStream | The NullStream acts as an empty stream object that may be returned by the NullResourceLocator. It does not open any files |
| CStringResourceStream | The StringResourceStream is a wrapper class for a std::stringstream that can be used to construct a resource. Useful when reading the resource stream in to memory (e.g. from a database or from multiple files) before trying to construct the resource |
| CFallbackConfiguration | The FallbackConfiguration class describes how a resource should be created if the ResourceManager is not being used, i.e., if resources have been specified through flags on the command line instead of through a resource-definition file |
| CFallbackConfigurationCreator | The FallbackConfigurationCreator plays the role in the ResourceManager framework of gluing a "resource_description" string and a FallbackConfiguration together |
| CFallbackConfigurationFactory | The FallbackConfigurationFactory is a singleton factory with which FallbackConfigurationCreator objects should be registered. The "fallback" system serves as a mechanism for preserving command-line functionality even while switching more protocols from requesting resources from the ResourceManager rather than reading directly from the command line |
| CFallbackConfigurationRegistrator | The FallbackConfigurationRegistrator class is a simple templated registration class that will, at construction, create a FallbackConfiguration and register it with the FallbackConfigurationFactory |
| CJobOptions | The JobOptions class holds job-specific options (i.e. command line flags). It can be used by the ResourceManager to hold options for a particular job, so that the ResourceManager can retrieve those options as needed. It is basically a bag for 12 OptionKey/OptionKeyValue maps, one for every kind of OptionKey |
| CLazyResourceManager | This is a mule class, meant to be derived from. It's job is to hold ResourceOptions and ResourceLocator objects by name (tag) as well as the ResourceConfigurations which serve as complete descriptions for how to construct a Resource. It should be thought of as a mule by classes that derive from it: it won't do anything on its own, but it can be directed to do things. The point of the class is to ake it easier to create ResourceManagers besides the JD2ResourceManager, which, at the time of this documentation, is the only class that derives from the LazyResourceManager |
| CResourceConfiguration | The set of strings necessary to describe how a resource should be constructed |
| CResourceLoader | The ResourceLoader is responsible for instantiating a Resource object and initializing it. In order to do so, the ResourceLoader is given an input stream and a ResourceOptions object. Note that the ResourceOptions object has to be of the right type, or the ResourceLoader will not be able to read the data that it needs out of it. If the ResourceLoader is given the wrong kind of ResourceOptions object, it will throw an exception |
| CResourceLoaderCreator | Instantiates a ResourceLoader as part of the ResourceLoaderFactory scheme. Derived classes should be registered with the ResourceLoaderFactory in one of the library init.cc files with a ResourceLoaderRegistrator |
| CResourceLoaderFactory | Instantiates ResourceLoaders. Creators may be registered with the Factory at any point, though it is recommended they be registered at load time. If two Creators are registered and they both give the same name for the ResourceLoader they say they will instantiate, then the Factory will exit with an error message |
| CResourceLoaderRegistrator | The ResourceLoaderRegistrator class is a simple templated registration class that will, at construction, create a ResourceLoader and register it with the ResouceLoaderFactory |
| CResourceLocator | ResourceLocator classes are responsible for retrieving data from a data store that will be used to construct a Resource. This data store could be a file system or a database or any other place where data is stored |
| CResourceLocatorCreator | The ResourceLocatorCreator class serves to link the name of a locator type and the (derived) ResourceLocator class that's responsible for retrieving data from a data store |
| CResourceLocatorFactory | The ResourceLocatorFactory instantiates ResourceLocator objects given their corresponding locator-type strings. It uses the load-time factory registration scheme, meaning that it is a singleton and takes an instance of a Creator object (a ResourceLocatorCreator) in its "factory_register" method. Templated instances of the ResourceLocatorRegistrator classes should be placed in the library init.cc files (e.g. core/init/init.cc or protocols/init/init.ResourceLocatorRegistrators.ihh) |
| CResourceLocatorRegistrator | The ResourceLocatorRegistrator gives an instance of a ResourceLocatorCreator to the ResourceLocatorFactory in its constructor, calling the ResourceLocatorFactory's factory_register() method. This call is actually accomplished by the WidgetRegistrator parent class. A single (templated) instance of this class for each ResourceLocatorCreator should be placed in the appropriate init.cc file (i.e. ResourceLocatorCreators that live in the protocols library should be put in src/protocols/init/init.ResourceLocatorRegistrators.ihh) |
| CResourceManager | The ResourceManager is a singleton class responsible for holding, distributing, and eventually deallocating resources which may be shared between multiple jobs. A protocol may communicate directly with the ResourceManager, requesting resources, but remaining unaware of where those resources came from, or whether the same resource is being used in multiple contexts |
| CResourceManagerCreator | Derived classes will be used by the ResourceManagerFactory to decide which of the various ResourceManagers should be instantiated. The ResourceManager is a singleton, but, different ResourceManagers can be instantiated in different contexts |
| CResourceManagerFactory | A factory class for managing the instantiation of the singleton ResourceManager: only one of the various derived classes will be instantiated. Currently, it asks for the JD2ResourceManager; in the future, this should be fixed so that it reads from the options system to figure out which ResourceManager to instantiate |
| CResourceManagerRegistrator | The ResourceManagerRegistrator creates an instantiate of the templated ResourceManagerCreator class and gives it to the ResourceManagerFactory. A single instance for each ResourceManagerCreator should be put in the appropriate init.cc file |
| CResourceOptions | The ResourceOptions class is responsible for describing all the data requried for instanting a particular resource, except for the data stream (i.e. the file) that contains the data for the resource. For example, when reading in a PDB file, there are 30 different options for how that PDB file should be turned into a Pose. That data is now held in an ImportPoseOptions object. The purpose of the ResourceOptions class is to allow different jobs to load resources in different ways, or for one job to load two different resources of the same type in different ways. For example, a protocol may need both a centroid pose and a fullatom pose to be loaded in from disk; however, if the logic for loading a pose in from disk is controlled by the options system alone, this becomes impossible |
| CResourceOptionsCreator | Each derived ResourceOptionsCreator class is responsible for instantiating a (specific) derived ResourceOptions class, and for telling the ResourceOptionsFactory the string which identifies that class. There should be one derived ResourceOptionsCreator class for each ResourceOptions class |
| CResourceOptionsFactory | The ResourceOptionsFactory class is responsible for maintaining the map between the names of the ResourceOptions classes (strings) and the ResourceOptionsCreator classes that are responsible for instantiating the ResourceOption classes. This is a singleton class. It is initialized at load time – or at least after the call to devel::init( argc, argv ) – and populated with the help of ResourceOptionsRegistrator instances |
| CResourceOptionsRegistrator | The ResourceOptionsRegistrator class is responsible for creating an instance of the (templated) ResourceOptionsCreator class and giving it to the ResourceOptionsFactory in its construtor. Instances of this class placed in the init.cc files (e.g. core/init/init.cc) ensure that the ResourceOptionsFactory is fully populated with the ResourceOptionsCreators by the time that the call to devel::init() completes |
| CResourceStream | The ResourceStream represents an abstract class for packaging up a standard istream so that data that the ResourceLocator needs to deliver to a ResourceLoader can come from arbitrary sources (e.g. from either a file or from a database) |
| ►Nsampling | |
| ►Norientations | |
| CPermute | |
| CQuatDBMetadata | |
| CQuaternion | |
| CQuaternionGrid | |
| CQuaternionGridManager | |
| CQuatSet | |
| CTriple | |
| ►Nsvd | |
| CSVD_Solver | |
| ►Cbasic_otstream | Base class for Tracer, TracerProxy and UTracer objects |
| Cbasic_tstringbuf | Inner class declaration |
| CComparingTracer | |
| CDynamicProfileThis | |
| CEmitter | Lightweight class to ease writting YAML documents (http://yaml.org) |
| CExecutionResult | Struct that hold result code + output of external process |
| CJsonEmitter | Lightweight class to ease writting JSON documents, a subset of YAML (http://json.org) |
| CMemTracer | |
| CMetricValue | |
| CMetricValueBase | |
| CProfileThis | |
| CPyTracer | Special PyRosetta friendly Tracer like buffer. Use it to capture Tracer output with set_ios_hook |
| CReport | Data class to hold Report information. Use Reporter class for write access |
| CReporter | Proxy class to access Reporter class though OP. Allow null OP on init (all reporter function in this case do nothing) |
| ►CTracer | Class for handling user debug/warnings/errors. Use instance of this class instead of 'std::cout' for all your regular io. Channel argument must be related to the location of the source file. For example if you create Tracer object in src/basic/scoring/myfile.cc, then channel must be something like 'src.basic.scoring.myfile' |
| CTracerProxy | Small inner class acting as a proxy to an object that hold it |
| CTracerManager | Simple singleton class to hold the all_tracers_ array, which otherwise suffers from funky double-construction problems when declared as a static data member of Tracer |
| CTracerOptions | Data structure to store all system level options for Tracer system |
| CTracerToFile | |
| CYamlEmitter | Emitter for more classically formatted YAML |
| ►Nbinder | |
| CBinder | Bindings Generator - represent object that can generate binding info for function, class, enum or data variable |
| CClassBinder | |
| CConfig | |
| CContext | Module - represent bindings of individual Python module |
| CEnumBinder | |
| CFunctionBinder | |
| CIncludeSet | |
| Cmap_binder | |
| Cvector_binder | |
| ►Nblivens | |
| ►Nboost_adaptbx | |
| ►Npython | |
| Cistream | |
| Costream | |
| Cpython_istream_wrapper | |
| Cpython_ostream_wrapper | |
| ►Cstreambuf | A stream buffer getting data from and putting data into a Python file object |
| Cistream | |
| Costream | |
| Cstreambuf_capsule | |
| ►NBuildBindings | |
| CModuleBuilder | |
| CNT | |
| CSubCall | |
| ►NBuildPackagedBindings | |
| CModuleBuilder | |
| ►Ncalccontacts | |
| Catom_contact | |
| CcontactProtein | |
| CresContact | |
| CshellAtom | |
| ►Ncanonical_sampling | |
| ►Ncarbohydrates | |
| ►Ncm | |
| ►Ncmiles | |
| ►Ncore | |
| ►Noptions | |
| ►Ncorrections | |
| ►Ndemo | |
| ►Ndevel | |
| CVersionRegistrator | |
| ►Ndna | |
| ►Ndesign | |
| ►Ndocking | |
| ►Nligand | |
| ►Nflexpack | |
| ►NFloppyTail | |
| ►Nflxbb | |
| ►Nfmt | |
| ►Ninternal | |
| CArg | |
| CArgArray | |
| CArgFormatter | |
| CArgMap | |
| CArgType | |
| CArgVisitor | |
| CBasicArgFormatter | |
| CBasicCharTraits | |
| CBasicData | |
| CCharTraits | |
| CCharTraits< char > | |
| CCharTraits< wchar_t > | |
| CConditional | |
| CConditional< false, T, F > | |
| CConvertToInt | |
| CConvertToIntImpl | |
| CConvertToIntImpl2 | |
| CConvertToIntImpl2< T, true > | |
| CConvertToIntImpl< T, true > | |
| CDummyInt | |
| CDummyStream | |
| CEnableIf | |
| CEnableIf< true, T > | |
| CFixedBuffer | |
| CFormatBuf | |
| CFormatterBase | |
| CIntTraits | |
| CMakeUnsigned | |
| CMakeValue | |
| CMemoryBuffer | |
| CNamedArg | |
| CNot | |
| CNot< false > | |
| CNull | |
| CPrintfArgFormatter | |
| CPrintfFormatter | |
| CRuntimeError | |
| CSignChecker | |
| CSignChecker< false > | |
| CTypeSelector | |
| CTypeSelector< false > | |
| ►CValue | |
| CCustomValue | |
| CStringValue | |
| CWCharHelper | |
| CWCharHelper< T, wchar_t > | |
| CAlignSpec | |
| CAlignTypeSpec | |
| CArgList | |
| CBasicArrayWriter | |
| CBasicCStringRef | |
| CBasicFormatter | |
| CBasicMemoryWriter | |
| CBasicStringRef | |
| CBasicWriter | |
| CBuffer | |
| ►CBufferedFile | |
| CProxy | |
| CEmptySpec | |
| CErrorCode | |
| ►CFile | |
| CProxy | |
| CFormatError | |
| CFormatInt | |
| CFormatSpec | |
| CIntFormatSpec | |
| CStrFormatSpec | |
| CSystemError | |
| CTypeSpec | |
| CWidthSpec | |
| ►Nfrags | |
| ►Nfull_model | |
| ►Nin | |
| ►Ninout | |
| ►Nio | |
| ►Nlh | |
| ►NloadPDB | |
| CchainType | |
| Cnew_PDBatom | |
| CPDBatom | |
| CPDBres | |
| CProtein | |
| CProteinChain | |
| ►Nloops | |
| ►Nmagnesium | |
| ►Nmatdes | |
| ►Nmh | |
| ►Nmistakes | |
| ►Nmp | |
| ►Nbenchmark | |
| ►Nms | |
| ►Nnumeric | Unit headers |
| ►Nalignment | |
| CQCP_Kernel | |
| ►Nconstants | |
| ►Ncoordinate_fitting | |
| CCoordinateArray_RMSD_FlatLookup | |
| CFlatLookup | |
| ►Nexpression_parser | |
| CAbsoluteValueExpression | |
| CAddExpression | |
| CAndExpression | |
| CArithmeticASTExpression | |
| CArithmeticASTFactor | |
| CArithmeticASTFunction | |
| CArithmeticASTNode | Base class for Abstract Syntax Tree (AST) for the simple Arithmetic language defined here |
| CArithmeticASTRestExpression | |
| CArithmeticASTRestTerm | |
| CArithmeticASTTerm | |
| CArithmeticASTValue | Either a variable or a literal |
| CArithmeticScanner | |
| CASTPrinter | Traverse the AST and print it to standard out |
| CASTVisitor | Double-dispatch visitor pattern for abstract syntax tree |
| CBinaryExpression | |
| CBooleanExpressionCreator | |
| CBooleanExpressionScanner | |
| CDivideExpression | |
| CEqualsExpression | |
| CExpression | Pure virtual base class to define arbitrary expressions for scripting arithmetic operations (e.g. addition and multipliction) |
| CExpressionCreator | Class to traverse the abstract syntax tree produced by the parsing of a properly-formed string in the Arithmetic expression language. Produces an Expression tree capable of performing arithmetic. Connects the "variable" nodes in this tree to the owning WrapperOptEMultifunc so that their values can be retrieved during expression evaluation inside the WrapperOptEMultifunc functor |
| CFunctionToken | |
| CGT_Expression | Greater Than |
| CGTE_Expression | Greater Than or Equal To |
| CITEExpression | |
| CLiteralExpression | |
| CLiteralToken | |
| CLT_Expression | Less Than |
| CLTE_Expression | Less Than or Equal To |
| CMaxExpression | |
| CMetaMaxExpression | Evaluates ee1 when e1 is larger than e2; evaluates ee2 otherwise |
| CMetaMinExpression | Evaluates ee1 when e1 is less than e2; evaluates ee2 otherwise |
| CMinExpression | |
| CMultiplyExpression | |
| CNaryExpression | |
| CNotExpression | |
| COrExpression | |
| CSimpleExpressionCreator | |
| CSimpleToken | |
| CSquarerootExpression | |
| CSubtractExpression | |
| CToken | |
| CTokenSet | |
| CUnaryExpression | |
| CVariableExpression | |
| CVariableToken | |
| ►Nfourier | |
| Ckiss_dct_state | |
| Ckiss_fft_state | |
| Ckiss_fftnd_state | |
| Ckiss_fftndr_state | |
| Ckiss_fftr_state | |
| Ckiss_fftsplit_state | |
| CSHT | |
| CSO3coeffs | |
| ►Ngeometry | |
| ►Nhashing | |
| CBall | |
| Cbin_index_hasher | Small hashing struct with no private data; simply an algorithm to turn a 64-bit representation of a 6d voxel into an integer |
| CCounter | |
| CSixDCoordinateBinner | Bin the six degrees of freedom that describe the downstream geometry of a hit. These degrees of freedom are, in order, the x, y and z coordinates of orientation atom3, and the phi, psi, and theta euler angles that describe the orientation of the coordinate frame at orientation atom 3. The binner is responsible for maintaining the lower corner of the 6-d space – the first two Euler angles wrap at 360; the third Euler angle, theta, does not wrap in the same way. See the comments for the bin6 method |
| CSixDOffsetTree | Returns a list of offsets corresponding to the bins in a hypershell with radius x |
| ►CxyzStripeHash | |
| Cconst_iterator | |
| Citer_base | |
| Cushort2 | |
| ►CxyzStripeHashWithMeta | |
| Cfloat4 | |
| Citer_base | |
| Cmeta_iterator | |
| Cushort2 | |
| Cxyz_iterator | |
| Cxyzmeta_iterator | |
| CxyzStripeHashWithMeta_float | |
| CBoundingBox | 3d axis aligned bounding box class |
| ►Nhistograms | |
| COneDHistogram | |
| CTwoDHistogram | |
| ►Ninterpolation | |
| ►Nperiodic_range | |
| ►Nspline | |
| CBicubicSpline | |
| Ccompare_interp_range | |
| CCompoundInterpolator | |
| CCubicSpline | |
| Cinterp_range | |
| CInterpolator | |
| CLinearFunction | |
| COrderPoint | |
| CPoint | |
| CPolycubicSpline | |
| CSimpleInterpolator | |
| CSplineGenerator | |
| CTricubicSpline | |
| CHistogram | A histogram with fixed-width bins |
| CHistogramAP | |
| CHistogramCAP | |
| CHistogramCOP | |
| CHistogramOP | |
| ►Nkdtree | |
| CCompareKDPoints | |
| CHyperRectangle | |
| CKDNode | |
| CKDPoint | |
| CKDPoint_MinDist | |
| CKDPointList | Class for keeping track of the closest N KDPoint objects by distance |
| CKDTree | |
| CWrappedPrimitive | |
| ►Nkinematic_closure | |
| Cp | |
| ►Nlinear_algebra | |
| CGeneralizedEigenSolver | Solves generalized eigenvalue problems |
| ►Nmodel_quality | |
| CRmsData | RmsData is a class intended to replace the global rms_obj namespace from rosetta++. Initial implementation is with a singleton design pattern to mimic a global namespace from rosetta++ |
| ►Nnls | |
| Clm_control_struct | |
| Clm_status_struct | |
| ►Nrandom | |
| CDistributionSampler | |
| Cmt19937_RG | |
| CRandomGenerator | Random number generator system |
| CReservoirSampler | Simple container for keeping K random values |
| Cstandard_RG | Generator based on rand() < clib > function |
| Cuniform_RG | Uniform random number generator |
| CWeightedReservoirItem | |
| CWeightedReservoirSampler | |
| CWeightedSampler | |
| CAgglomerativeHierarchicalClusterer | |
| CAverageLinkClusterer | |
| CBodyPosition | Rigid body 3-D position/transform |
| CCalculator | |
| CCalculatorParser | |
| CClusteringTreeNode | |
| CClusterOptions | |
| CColPointers | |
| CColsPointer | |
| CColVectors | |
| CCompleteLinkClusterer | |
| CEulerAngles | Euler angles 3-D orientation representation |
| CFastRemainderSelector | Fast remainder function selector class for non-integer types |
| CFastRemainderSelector< T, true > | Fast remainder function selector class for integer types |
| CHomogeneousTransform | |
| CHomogeneousTransform_Double | |
| CIntervalSet | |
| CIntervalSet_Double | |
| CIOTraits | Numerics input/output type traits |
| CIOTraits< double > | Numerics input/output type traits double specialization |
| CIOTraits< float > | Numerics input/output type traits float Specialization |
| CIOTraits< int > | Numerics input/output type traits int specialization |
| CIOTraits< long double > | Numerics input/output type traits long double specialization |
| CIOTraits< long int > | : Numerics input/output type traits long int specialization |
| CIOTraits< short int > | Numerics input/output type traits short int specialization |
| CIOTraits< unsigned int > | : Numerics input/output type traits unsigned int specialization |
| CIOTraits< unsigned long int > | Numerics input/output type traits unsigned long int specialization |
| CIOTraits< unsigned short int > | : Numerics input/output type traits unsigned short int specialization |
| CMathMatrix | |
| CMathNTensor | |
| CMathTensor | |
| CMathVector | |
| CModSelector | Mod function selector class for non-integer types |
| CModSelector< T, true > | Mod function selector class for integer types |
| CModuloSelector | Modulo function selector class for non-integer types |
| CModuloSelector< T, true > | Modulo function selector class for integer types |
| CMultiDimensionalHistogram | Class for accumulating a histogram of one or more numeric variables |
| CNearestSelector | Nearest function selector class for R non-integer or T integer |
| CNearestSelector< R, T, true > | Nearest function selector class for R integer and T non-integer |
| CNumericTraits | NumericTraits: Numeric type traits |
| CNumericTraits< double > | NumericTraits: Numeric type traits double specialization |
| CNumericTraits< float > | NumericTraits: Numeric type traits float specialization |
| CNumericTraits< long double > | NumericTraits: Numeric type traits long double specialization |
| CPolynomial_1d | |
| CPy_xyzTransform_double | |
| CQuaternion | Unit quaternion 3-D orientation representation |
| CRemainderSelector | Remainder function selector class for non-integer types |
| CRemainderSelector< T, true > | Remainder function selector class for integer types |
| CRocCurve | |
| CRocPoint | |
| CRowPointers | |
| CRowsPointer | |
| CRowVectors | |
| CSingleLinkClusterer | |
| CsphericalVector | SphericalVector: Fast spherical-coordinate numeric vector |
| CUniformRotationSampler | |
| Curs_Quat | |
| CXformHash32 | |
| CXformHash64 | |
| CXforms | |
| CxyzMatrix | XyzMatrix: Fast 3x3 xyz matrix template |
| ►CxyzTransform | |
| CLine | |
| CPlane | |
| CxyzTriple | Fast (x,y,z)-coordinate vector container |
| CxyzVector | XyzVector: Fast (x,y,z)-coordinate numeric vector |
| ►NObjexxFCL | |
| ►Nformat | |
| CBite | |
| CSkip | |
| ►Ninternal | |
| CInitializerSentinel | InitializerSentinel: FArray Constructor Initializer Sentinel Class |
| CObserverGraph | ObserverGraph: Observer Graph Representation |
| CProxySentinel | ProxySentinel: FArray Constructor Proxy Sentinel Class |
| Cbyte | Byte: One-Byte Integer |
| CCArray | CArray: Memory-Managed C Array Wrapper |
| CCArrayP | CArrayP: Memory-Managed C Array Wrapper Supporting Proxies |
| CChunk | Chunk: Contiguous Array for Use in ChunkVector |
| CChunkExponent | ChunkExponent: ChunkVector Exponent Wrapper for Function Disambiguation and Range Clipping |
| CChunkVector | ChunkVector: Chunk-Contiguous Vector for Fast Very Large Vectors |
| CCstring | Cstring: C String Wrapper |
| CDimension | Dimension: Dynamic Dimension |
| CDimensionExpression | DimensionExpression: DimensionExpression Interface Class |
| CDimensionExpressionCon | DimensionExpressionCon: Constant-Valued DimensionExpression |
| CDimensionExpressionCube | DimensionExpressionCube: DimensionExpression Cube Function |
| CDimensionExpressionDiv | DimensionExpressionDiv: DimensionExpression Binary Division |
| CDimensionExpressionMax | DimensionExpressionMax: DimensionExpression Binary Max Function |
| CDimensionExpressionMin | DimensionExpressionMin: DimensionExpression Binary Min Function |
| CDimensionExpressionMul | DimensionExpressionMul: DimensionExpression Binary Product |
| CDimensionExpressionPow | DimensionExpressionPow: DimensionExpression Power Function: expression1^expression2 |
| CDimensionExpressionRef | DimensionExpressionRef: Dimension Reference DimensionExpression |
| CDimensionExpressionSquare | DimensionExpressionSquare: DimensionExpression Square Function |
| CDimensionExpressionSub | DimensionExpressionSub: DimensionExpression Binary Subtraction |
| CDimensionExpressionSum | DimensionExpressionSum: DimensionExpression Binary Sum |
| CDynamicIndexRange | DynamicIndexRange: Dynamic Index Range |
| CFArray | FArray: Fortran-Compatible Array Hierarchy Abstract Base Class |
| CFArray1 | FArray1: Fortran-Compatible 1D Array Abstract Base Class |
| CFArray1A | FArray1A: Fortran-Compatible 1D Argument Array |
| CFArray1D | FArray1D: Fortran-Compatible 1D Array |
| CFArray1P | FArray1P: Fortran-Compatible 1D Proxy Array |
| CFArray2 | FArray2: Fortran-Compatible 2D Array Abstract Base Class |
| CFArray2A | FArray2A: Fortran-Compatible 2D Argument Array |
| CFArray2D | FArray2D: Fortran-Compatible 2D Array |
| CFArray2P | FArray2P: Fortran-Compatible 2D Proxy Array |
| CFArray3 | FArray3: Fortran-Compatible 3D Array Abstract Base Class |
| CFArray3A | FArray3A: Fortran-Compatible 3D Argument Array |
| CFArray3D | FArray3D: Fortran-Compatible 3D Array |
| CFArray3P | FArray3P: Fortran-Compatible 3D Proxy Array |
| CFArray4 | FArray4: Fortran-Compatible 4D Array Abstract Base Class |
| CFArray4A | FArray4A: Fortran-Compatible 4D Argument Array |
| CFArray4D | FArray4D: Fortran-Compatible 4D Array |
| CFArray4P | FArray4P: Fortran-Compatible 4D Proxy Array |
| CFArray5 | FArray5: Fortran-Compatible 5D Array Abstract Base Class |
| CFArray5A | FArray5A: Fortran-Compatible 5D Argument Array |
| CFArray5D | FArray5D: Fortran-Compatible 5D Array |
| CFArray5P | FArray5P: Fortran-Compatible 5D Proxy Array |
| CFArray6 | FArray6: Fortran-Compatible 6D Array Abstract Base Class |
| CFArray6A | FArray6A: Fortran-Compatible 5D Argument Array |
| CFArray6D | FArray6D: Fortran-Compatible 5D Array |
| CFArray6P | FArray6P: Fortran-Compatible 5D Proxy Array |
| CFArrayInitializer | FArrayInitializer: FArray Initializer Class Template |
| CFArraySection | FArraySection: Fortran-Compatible Array Section Proxy |
| CFArrayTraits | FArrayTraits: FArray Traits Template |
| CFArrayTraits< numeric::xyzVector< T > > | Specialization for FArrayTraits, to allow reasonable default constructor in FArray context |
| CFastRemainderSelector | Fast remainder function selector class for non-integer types |
| CFastRemainderSelector< T, true > | Fast remainder function selector class for integer types |
| CFstring | Fstring: Fixed-Length Fortran-Compatible String |
| CFsubstring | Fsubstring: Fixed-Length Fortran-Compatible Substring |
| CIndexRange | IndexRange: Index Range Abstract Base Class |
| CKeyFArray1D | KeyFArray1D: Key-Access Fortran-Compatible 1D Array |
| CKeyFArray2D | KeyFArray2D: Key-Access Fortran-Compatible 2D Array |
| CKeyFArray3D | KeyFArray3D: Key-Access Fortran-Compatible 3D Array |
| CKeyFArray4D | KeyFArray4D: Key-Access Fortran-Compatible 4D Array |
| CKeyFArray5D | KeyFArray5D: Key-Access Fortran-Compatible 5D Array |
| CKeyFArray6D | KeyFArray6D: Key-Access Fortran-Compatible 6D Array |
| CModSelector | Mod function selector class for non-integer types |
| CModSelector< T, true > | Mod function selector class for integer types |
| CModuloSelector | Modulo function selector class for non-integer types |
| CModuloSelector< T, true > | Modulo function selector class for integer types |
| CNearestSelector | Nearest function selector class for R non-integer or T integer |
| CNearestSelector< R, T, true > | Nearest function selector class for R integer and T non-integer |
| CObserver | Observer: Combined Subject + Observer Abstract Base Class |
| CObserverMulti | ObserverMulti: Combined Subject + Multi Observer Abstract Base Class |
| CObserverSingle | ObserverSingle: Combined Subject + Single Observer Abstract Base Class |
| CRemainderSelector | Remainder function selector class for non-integer types |
| CRemainderSelector< T, true > | Remainder function selector class for integer types |
| CSetWrapper | SetWrapper: Insulating Wrapper of std::set That Can Be Forward Declared |
| CStar | Star: Sentinel for Assumed Size Array Upper Bound |
| CStaticIndexRange | StaticIndexRange: Static Index Range |
| CTypeTraits | TypeTraits: Type Traits Template |
| CTypeTraits< double > | TypeTraits: Type Traits double Specialization |
| CTypeTraits< float > | TypeTraits: Type Traits float Specialization |
| CTypeTraits< int > | TypeTraits: Type Traits int Specialization |
| CTypeTraits< long double > | TypeTraits: Type Traits long double Specialization |
| CTypeTraits< long int > | TypeTraits: Type Traits long int Specialization |
| CTypeTraits< short int > | TypeTraits: Type Traits short int Specialization |
| CTypeTraits< unsigned int > | TypeTraits: Type Traits unsigned int Specialization |
| CTypeTraits< unsigned long int > | TypeTraits: Type Traits unsigned long int Specialization |
| CTypeTraits< unsigned short int > | TypeTraits: Type Traits unsigned short int Specialization |
| Cubyte | Ubyte: One-Byte Integer |
| ►NoptE | |
| ►Noptions | |
| CKeepSameFile | |
| ►Noptions_class | |
| COption | |
| ►Nout | |
| ►Npacking | |
| ►NPDBInfo | |
| CPDB | |
| ►NpH | |
| ►NPhiPsi | |
| CATOMinfo | |
| ►Nplatform | Fixed size types |
| ►Npose_metrics | |
| ►Nprotocols | |
| ►NPyMOLPyRosettaServer | |
| CMatrix | |
| CPlanePoints | |
| CPR_PyMOLServer | |
| CPR_UDPServer | |
| CStartUpError | Exceptions |
| CXYZCoord | |
| ►Npyrosetta | |
| ►Ntoolbox | |
| ►Ngenerate_resfile | |
| CResfileWriter | |
| CCD | |
| CEnergyMethod | |
| CPyJobDistributor | |
| CPyRosettaException | Exception handling |
| CPythonPyExitCallback | |
| ►Nrelax | |
| ►Nremodel | |
| ►Nrna | |
| ►Nfarna | |
| ►Nrosetta_binders | |
| ►Nhas_insertion_operator_implementation | |
| Cany_type | |
| Chas_equal_operator_s | |
| Chas_equal_operator_s< std::map< A, B > > | |
| Chas_equal_operator_s< std::pair< A, B > > | |
| Chas_equal_operator_s< std::set< A > > | |
| Chas_equal_operator_s< std::vector< A > > | |
| Chas_equal_operator_s< T > | |
| Chas_equal_operator_s< utility::vector0< A > > | |
| Chas_equal_operator_s< utility::vector1< A > > | |
| Chas_insertion_operator_s | |
| Cutility_vector_binder | |
| ►Nrosetta_scripts | |
| CRosetta_Script_Creator | |
| ►Nscore | |
| ►Nscoring | |
| ►Nsetup | |
| CPyRosettaDistribution | |
| CRosettaDistribution | |
| ►Nsidechain_cst_3 | |
| CAtom | |
| CResidue | |
| ►Nsrc | |
| ►Ncore | |
| ►Nprotocols | |
| ►Njd2 | |
| CRosettaScriptWrapper | |
| ►NPyMolLink | |
| CPyMOLMover | |
| CPyMOLObserver | |
| CPySocketClient | Classes |
| ►Nutility | |
| CPyRosettaException | |
| CPythonPyExitCallback | |
| CCD | |
| CEnergyMethod | |
| CPyJobDistributor | |
| CPyRosettaException | Exception handling |
| CPythonPyExitCallback | |
| ►Nstd | STL namespace |
| Cnumeric_limits< fmt::internal::DummyInt > | |
| ►Nstepwise | |
| ►Nmonte_carlo | |
| ►Ntemplates | |
| ►Ntest | |
| ►NT007_TracerIO | |
| CMyPyTracer | |
| ►NT850_SubClassing | |
| CA | |
| CMy_New_Mover | |
| CMyNewCI1B | |
| CMyNewCI1B_Creator | |
| CPyOverloadTest | |
| CPyValue | |
| ►NT860_SubClassing_EnergyMethods | |
| CMyCI1B_Method | |
| ►NT870_SubClassing_EnergyMethods2 | |
| CCD2B_Method | |
| CCI1B_Method | |
| CCI2B_Method | |
| ►NWorkshop9_my_shapes | |
| CCI2BScoreMethod | |
| CLengthScoreMethod | |
| CMyCircle | |
| CMyShape | |
| CMySquare | |
| CPhiNByXDegreesMover | |
| ►Ntests | |
| ►Ntest_basic | |
| CTestInitialization | |
| ►Ntoolbox | |
| ►Ngenerate_resfile | |
| CResfileWriter | |
| ►Ntools | |
| ►NCppParser | |
| CCD | |
| CClangXML | |
| CCppClass | |
| CCppEnum | |
| CCppFunction | |
| CCppNamespace | |
| CCppType | |
| CCppType_Complex | |
| CCppType_Composite | |
| CCppType_Fundamental | |
| CCppType_Simple | |
| CCppType_Typedef | |
| CCppVariable | |
| CGccXML | |
| CNamespace | |
| CReferenceSection | |
| ►Ndox_extract | |
| Cdox_extract | |
| ►NDoxygenExtractorPyPP | |
| Cdoxygen_doc_extractor | |
| ►Nufv | |
| ►Nutility | Comment 0 |
| ►Nexcn | |
| CEXCN_BadInput | |
| CEXCN_Base | |
| CEXCN_Exception | |
| CEXCN_FileNotFound | |
| CEXCN_IO | |
| CEXCN_JD2Failure | |
| CEXCN_KeyError | |
| CEXCN_Msg_Exception | |
| CEXCN_NullPointer | |
| CEXCN_RangeError | |
| CEXCN_RosettaScriptsOption | |
| ►Nfactory | |
| CFactory | Pluggable factory |
| CRegistrant | Factory registrant |
| CWidgetFactory | Factory base class holds a map between strings and owning pointers of the creator classes |
| CWidgetRegistrator | This class will register a Creator with a Factory at load time |
| ►Nfile | |
| CFileName | File name class supporting Windows and UN*X/Linux format names |
| CPathName | Path name class supporting Windows and UN*X/Linux format names |
| ►Ngraph | |
| CEXCN_Stop_BFS | Class to raise to do an immediate stop of a breadth first search. ONLY THROW FROM WITHIN A VISITOR PASSED TO breadth_first_visit_prune/breadth_first_search_prune |
| CHideVertexVisitor | |
| Cnull_bfs_prune_visitor | |
| CRingDetection | Basic chemical Bond |
| CRingEdgeAnnotationVisitor | |
| CRingSizeVisitor | A class to implement the behavior of the smallest ring size finding algorithm, accessible through the smallest_ring_size() function below |
| ►Nio | |
| ►Nmpi_stream | |
| Cbasic_mpi_ostream | A mpiper ostream |
| Cbasic_mpi_ostreambase | Base class for mpi ostreams |
| Cbasic_mpi_streambuf | A stream decorator that takes raw input and zips it to a ostream |
| CFileContentsMap | The FileContentsMap is a class that will minimize the number of times files are accessed from disk. The first time the contents of a file are requested, it will cache the contents the file in memory as a strings. All subsequent requests for the contents of that file will then be delivered without having to go to disk. WARNING: The FileContentsMap will not update the contents that it holds for a file after the first time it loads it, so if the contents change on disk, the FileContentsMap will be out of date |
| Cicstream | Icstream: Input channel stream wrapper class |
| Cirstream | Orstream: Input stream wrapper abstract base class |
| Cizstream | Izstream: Input file stream wrapper for uncompressed and compressed files |
| Cocstream | Ocstream: Output channel stream wrapper class |
| Corstream | Orstream: Output stream wrapper base class |
| Cozstream | Ozstream: Output file stream wrapper for uncompressed and compressed files |
| ►Njson_spirit | |
| ►Ninternal_ | |
| CType_to_type | |
| CConfig_map | |
| CConfig_vector | |
| CError_position | |
| CGenerator | |
| ►CJson_grammer | |
| Cdefinition | |
| CMulti_pass_iters | |
| CNull | |
| CPair_impl | |
| CSemantic_actions | |
| CStream_reader | |
| CStream_reader_thrower | |
| ►CValue_impl | |
| CVariant_converter_visitor | |
| ►Nkeys | |
| ►Nlookup | |
| Cbegin | Key lookup begin iterator functor |
| Cend | Key lookup end iterator functor |
| Cgen | Key lookup/generator functor |
| Chas | Key lookup has query functor |
| Ckey | Key lookup key query functor |
| Cn_key | Key lookup n_key query functor |
| CAutoKey | Automatic hidden index key abstract base class |
| CClassKeyMap | Keyed-access map with key subset map for each client class |
| CClassKeyVector | Keyed-access vector with key subset map for each client class |
| CKey | Hidden index key interface class |
| CKey2Tuple | 2-tuple meta-key |
| CKey2Vector | 2-key meta-key |
| CKey3Tuple | 3-tuple meta-key |
| CKey3Vector | 3-key meta-key |
| CKey4Tuple | 4-tuple meta-key |
| CKey4Vector | 4-key meta-key |
| CKeyCount | Key counter functor |
| CKeyLess | Key member comparison functor template |
| CKeyLookup | Key lookup map and collection |
| CKeyMapTraits | KeyMap traits class |
| CKeySetTraits | KeySet traits class |
| CKeyVector | Keyed-access vector |
| CKeyVectorTraits | KeyVector traits class |
| CNoClient | Default key policy class when no client is needed to distinguish key type |
| CPointerKeyLess | Key member comparison functor template for pointers |
| CSmallKeyMap | Keyed-access map with key subset map |
| CSmallKeyVector | Keyed-access vector with key subset map |
| CUserKey | User-created hidden index key abstract base class |
| CVariantKey | Variant key class |
| ►Nlibsvm | |
| CSvm_node_rosetta | |
| CSvm_rosetta | |
| ►Noptions | |
| ►NOptionKeys | |
| ►Noptions | Option display option keys |
| CAnyOption | Program any scalar-valued option abstract base class |
| CAnyOptionKey | Automatic hidden index key for any scalar-valued options |
| CAnyVectorOption | Program any vector-valued option abstract base class |
| CAnyVectorOptionKey | Automatic hidden index key for any vector-valued options |
| CBooleanOption | Program boolean option class |
| CBooleanOptionKey | Automatic hidden index key for boolean options |
| CBooleanVectorOption | Program boolean vector option class |
| CBooleanVectorOptionKey | Automatic hidden index key for boolean options |
| CFileOption | Program file option class |
| CFileOptionKey | Automatic hidden index key for file options |
| CFileVectorOption | Program file vector option class |
| CFileVectorOptionKey | Automatic hidden index key for file options |
| CIntegerOption | Program integer option class |
| CIntegerOptionKey | Automatic hidden index key for integer options |
| CIntegerVectorOption | Program integer vector option class |
| CIntegerVectorOptionKey | Automatic hidden index key for integer options |
| COption | Program option interface class |
| COptionCollection | Program options collection |
| COptionKey | Abstract automatic hidden index key for options |
| CPathOption | Program path option class |
| CPathOptionKey | Automatic hidden index key for path options |
| CPathVectorOption | Program path vector option class |
| CPathVectorOptionKey | Automatic hidden index key for path options |
| CRealOption | Program real option class |
| CRealOptionKey | Automatic hidden index key for real options |
| CRealVectorOption | Program real vector option class |
| CRealVectorOptionKey | Automatic hidden index key for real options |
| CResidueChainVectorOption | Program integer vector option class |
| CResidueChainVectorOptionKey | Automatic hidden index key for integer options |
| CScalarOption | Program scalar-valued option interface class |
| CScalarOption_T_ | Program scalar-valued option abstract base class |
| CScalarOptionKey | Abstract automatic hidden index key for scalar-valued options |
| CStringOption | Program string option class |
| CStringOptionKey | Automatic hidden index key for string options |
| CStringVectorOption | Program string option class |
| CStringVectorOptionKey | Automatic hidden index key for string options |
| CVariantOption | Variant option class |
| CVectorOption | Program vector-valued option interface class |
| CVectorOption_T_ | Program vector-valued option abstract base class |
| CVectorOptionKey | Abstract automatic hidden index key for vector-valued options |
| ►Npointer | |
| CReferenceCount | Base class for reference-counted polymorphic classes |
| ►Npy | |
| CBase | |
| CCOP_to_Python_converter | |
| COverloadTest | |
| CPyExitCallback | This class for holding callback function |
| CValue | |
| ►Nsignals | |
| CBufferedSignalHub | Forward declaration for SignalHub |
| CIsLinkUnitInvalid | Struct useful as combined predicate + deallocation of function object contained inside a LinkUnit |
| CLink | Interface wrapper around utility::signals::LinkUnit |
| CLinkUnit | Struct specifying actual link data between observers and subjects |
| CPausableSignalHub | Forward declaration for PausableSignalHub |
| CSignalHub | Forward declaration for SignalHub |
| CTokenHub | Forward declaration for TokenHub |
| ►Nsql_database | |
| CDatabaseMode | |
| CDatabaseSessionManager | |
| Csession | |
| Ctransaction | |
| CTransactionMode | |
| ►Ntag | |
| CTag | |
| CXMLErrorHandler | |
| CXMLSchemaAttribute | Class XMLSchemaAttribute represents what we refer to in Rosetta as an option for a tag. An attribute would reside inside of a tag, such as "scorefxn" in this tag (this XML Element): <MinMover name="min" scorefxn="talaris2014"> |
| CXMLSchemaComplexType | Class XMLSchemaComplexType represents the definition of the type for an element – that is, the structure of a set of elements with the same name. If an XMLSchemaElement is analogous to a utility::tag::Tag, an XMLSchemaComplexType is analogous to the wiki page describing the valid format for an instance of that Tag |
| CXMLSchemaComplexTypeGenerator | The XMLComplexTypeSchemaGenerator is used to define the schema for a complex type as they typically occurr in Rosetta |
| CXMLSchemaComplexTypeGeneratorImpl | |
| CXMLSchemaDefinition | The XMLSchemaDefinition class's purpose is to collect all of the elements that go into an XML Schema, to filter out the elements that are repeated (e.g. a restriction such as the "int_cslist" given in the description for XMLSchemaRestriction above may be reported twice to the XMLSchemaDefinition by several attributes that rely upon it), to detect non-identical duplicates that have the same name, and to write out the elements that it has been handed into a single string. The XMLSchemaDefinition is intended to be passed between static functions / non-class-member functions as a container for the XML Schema representations that these functions define. Such functions will always take an XMLSchemaDefinition reference as one of their input parameters. It is perfectly legitimate / recommended for one XML-schema-defining function that relies on a complexType or restriction that it does not itself define to pass its input XMLSchemaDefinition to the function that does define that complexType or restriction |
| CXMLSchemaElement | An XMLSchema element, e.g. the FixbbMover "tag" <FixbbMover name="fixbb" task_operations="ex1,ex2"> or the And element which contains a sub-element: <And><Chain id="A"></And>. An element can be defined with an unnamed complex type in-line, or it can say that its type is that of a complex type defined elsewhere. (In XML naming a tag is a single block beginning with "<" and ending with ">", so both "<And>" and "</And>" are tags. The block between the opening and closing tags is called an element. The utility::tag::Tag class represents a complete Element, and not simply the opening or closing tag of an element. This is certainly confusing |
| CXMLSchemaModelGroup | The ModelGroup covers four XML Schema model groups: xs:sequence, xs:choice, xs:all, and xs:group. A ModelGroup may contain any number of XMLSchemaParticles, interchanging between XMLElements and XMLModelGroups, BUT there are some fairly heavy restrictions on the xs:all model group, marginally enforced by this class and by XMLSchemaComplexType. This class is not exactly a top-level element, in that only xs:group is allowed to appear at the top level, but it is definitely worthwhile for this class to implement the write_definition funciton |
| CXMLSchemaParticle | This abstract class is meant to represent either an XMLSChemaElement or an XMLSchemaModelGroup so that the interchangable set of these objects in a ModelGroup can be represented. I may be misusing the term "particle" in the way that it is meant within XML Schema – so the mapping of this term to the term used in XML Schema is probably imperfect |
| CXMLSchemaRestriction | Class XMLSchemaRestriction describes a refinement on the behavior of existing types. For example, one could define a restriction representing a list of residue indexes separating commas: "15,44,102" and then describe an attribute of a complex type as having to conform to that restriction. An xml-schema validator would be able to say that an input file with "fifteen,fortyfour,onehundredandtwo" did not meet the schema |
| ►CXMLSchemaSimpleSubelementList | Defines an interface that can be used by those wishing to define a complexType that contains sub-elements. The structure of the XML Schema for the sub-elements will determined by how this list is given to the XMLSchemaComplexTypeGenerator. "simple" subelements are those which themselves contain no subelements (but may contain attributes). Also allowed are subelements that refer to previously-defined complexTypes or those that refer to previously defined xs:groups |
| CElementSummary | |
| CXMLSchemaTopLevelElement | The XMLSchemaTopLevelElement class signifies a class that could be written out as an XML element, with possible sub-elemets, in an XML schema. When generating a schema, the developer will hand an instance of a class derived from an XMLSchemaTopLevelElement to an XMLSchemaDefinition object |
| CXMLSchemaType | Class XMLSchemaType represents the name of a defined type that can be used to describe either an XMLElement or an XMLAttribute. It may refer to either a complex type or to a primative type or to a simple type |
| CXMLValidationOutput | |
| CA | A molecular system including residues, kinematics, and energies |
| CBitSet | Simple bit set |
| CBitVector | Simple bit vector |
| CBound | Bound value class |
| CCSI_Sequence | Class to hold all Terminal ASCII codes as static data for CSI_Sequence. Note: that on non-tty terminals all codes will initialized as empty to avoid polution of Rosetta logs |
| CDereferenceIterator | Const_iterator class for SilentFileData container |
| CEXCN_utility_exit | |
| Cfixedsizearray0 | |
| Cfixedsizearray0const_iterator | |
| Cfixedsizearray0iterator | |
| Cfixedsizearray1 | |
| Cfixedsizearray1const_iterator | |
| Cfixedsizearray1iterator | |
| CFixedSizeLexicographicalIterator | |
| Cheap | |
| Chistory_queue_struct | |
| Cin_place_list | |
| CInline_File_Provider | |
| CInline_File_Provider_Hook | |
| CLexicographicalIterator | |
| Clist_element | |
| COrderedTuple | The ordered tuple takes a container class T and defines comparison operators so that the tuple may be sorted |
| Cpredicate_cmp_filename | |
| CRawType | Meta-programming classes to provide the pointer type for down_cast |
| CRawType< T & > | |
| CRawType< T * > | |
| Crecent_history_queue | A class for keeping track of a subset of elements in a set that are pushed into a queue in a certain order, and which fall off the end of the queue in ther order in which they arrive. Elements in the set can be bumped to the front of the queue |
| CShow | |
| CSimulateMPI | Singleton class storing simulated MPI state |
| CSimulateMPIData | |
| CSimulateMPIMessage | |
| CSingletonBase | SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way |
| CSortFirst | |
| CSortSecond | |
| Csubset_mapping | This class handles the bookeeping to map between a set of integer ids in the "source" enumeration to a subset of those ids – the destination enumartion. Elements in the source enumeration that do not map to elements in the destination enumeration are represented by the value 0. Both enumerations should count from 1. Once the class has been initialized, this class offers O(1) mapping between elements in the enumerations |
| Cvector0 | Std::vector with assert-checked bounds |
| Cvector0< bool, A > | Std::vector with assert-checked bounds: bool specialization |
| Cvector1 | Std::vector with 1-based indexing |
| Cvector1< bool, A > | Std::vector with 1-based indexing: bool specialization |
| CvectorL | Std::vector with L-based indexing |
| CvectorL< L, bool, A > | Std::vector with L-based indexing: bool specialization |
| CvectorL_IndexSelector | VectorL index type selector: Nonnegative lower index non-specialization |
| CvectorL_IndexSelector< false > | VectorL index type selector: Negative lower index specialization |
| CvectorL_ZeroSelector | VectorL lower index zero selector: Nonzero lower index non-specialization |
| CvectorL_ZeroSelector< false > | VectorL lower index zero selector: Zero lower index specialization |
| ►Nyaml | |
| ►Ncomposer | |
| CComposer | |
| CComposerError | |
| ►Nconstructor | |
| CBaseConstructor | |
| ►CConstructor | |
| Cclassobj | |
| CConstructorError | |
| CSafeConstructor | |
| ►Ncyaml | |
| CCBaseDumper | |
| CCBaseLoader | |
| CCDumper | |
| CCLoader | |
| CCSafeDumper | |
| CCSafeLoader | |
| ►Ndumper | |
| CBaseDumper | |
| CDumper | |
| CSafeDumper | |
| ►Nemitter | |
| CEmitter | |
| CEmitterError | |
| CScalarAnalysis | |
| ►Nerror | |
| CMark | |
| CMarkedYAMLError | |
| CYAMLError | |
| ►Nevents | |
| CAliasEvent | |
| CCollectionEndEvent | |
| CCollectionStartEvent | |
| CDocumentEndEvent | |
| CDocumentStartEvent | |
| CEvent | |
| CMappingEndEvent | |
| CMappingStartEvent | |
| CNodeEvent | |
| CScalarEvent | |
| CSequenceEndEvent | |
| CSequenceStartEvent | |
| CStreamEndEvent | |
| CStreamStartEvent | |
| ►Nloader | |
| CBaseLoader | |
| CLoader | |
| CSafeLoader | |
| ►Nnodes | |
| CCollectionNode | |
| CMappingNode | |
| CNode | |
| CScalarNode | |
| CSequenceNode | |
| ►Nparser | |
| CParser | |
| CParserError | |
| ►Nreader | |
| CReader | |
| CReaderError | |
| ►Nrepresenter | |
| CBaseRepresenter | |
| CRepresenter | |
| CRepresenterError | |
| CSafeRepresenter | |
| ►Nresolver | |
| CBaseResolver | |
| CResolver | |
| CResolverError | |
| ►Nscanner | |
| CScanner | |
| CScannerError | |
| CSimpleKey | |
| ►Nserializer | |
| CSerializer | |
| CSerializerError | |
| ►Ntokens | |
| CAliasToken | |
| CAnchorToken | |
| CBlockEndToken | |
| CBlockEntryToken | |
| CBlockMappingStartToken | |
| CBlockSequenceStartToken | |
| CDirectiveToken | |
| CDocumentEndToken | |
| CDocumentStartToken | |
| CFlowEntryToken | |
| CFlowMappingEndToken | |
| CFlowMappingStartToken | |
| CFlowSequenceEndToken | |
| CFlowSequenceStartToken | |
| CKeyToken | |
| CScalarToken | |
| CStreamEndToken | |
| CStreamStartToken | |
| CTagToken | |
| CToken | |
| CValueToken | |
| CYAMLObject | |
| CYAMLObjectMetaclass | |
| ►Nzlib_stream | |
| Cbasic_unzip_streambuf | A stream decorator that takes compressed input and unzips it to a istream |
| Cbasic_zip_istream | A zipper istream |
| Cbasic_zip_istreambase | Base class for unzip istreams |
| Cbasic_zip_ostream | A zipper ostream |
| Cbasic_zip_ostreambase | Base class for zip ostreams |
| Cbasic_zip_streambuf | A stream decorator that takes raw input and zips it to a ostream |
| CA | |
| CA | |
| CA | |
| CA1 | |
| CA2 | |
| CA3 | |
| CA4 | |
| CAccess | |
| CAnchorFinderMover | AnchorFinder mover |
| CAPDBCMover | APDBC mover |
| Carray_scalar_converter | |
| CArrays | |
| CASTConsumer | |
| CASTFrontendAction | |
| CB | |
| CBase | |
| CBaseA | |
| CBaseB | |
| CBaseC | |
| CBaseD | |
| CBaseWrap | |
| CBinderASTConsumer | |
| CBinderFrontendAction | |
| CBinderVisitor | |
| ►CCache | |
| Chead_t | |
| CCaToAllAtom | |
| CCAtrace | |
| CClassVisitor | |
| CConsensusFragmentMover | |
| CConstOverload | |
| CContextDependentTwoBodyEnergy | |
| CCoupledMovesProtocol | |
| CDatabaseIOBenchmark | |
| Cdecision_function | |
| CDelete | |
| CDemoBase | |
| CDemoDerived | |
| CDerivedA | |
| CDerivedB | |
| CDerivedC | |
| CDerivedD | |
| CDesignBenchmark | |
| CDockFragmentsMover | |
| CDockingBenchmark | |
| CDougsDockDesignMinimizeMagicMover | |
| CDummyMover | Must have this after BOINC stuff to avoid windows build error |
| CEnums | |
| CException | |
| CExemplarMover | |
| CExposedStrandMover | |
| CExtractATD | |
| CFastRelaxPerformanceBenchmark | |
| CFitMover | |
| CFloating_point | |
| CFragID | |
| CFragInfo | |
| CFragmentAssemblyMover | |
| CHbsDesignMover | |
| CHDdesignMover | |
| CHDmakerMover | |
| CHistogram | |
| CHPatchByChainNPDCalculator | |
| CHPatchByChainNPDCalculatorCreator | |
| CHPatchNPDCalculator | |
| CHPatchNPDCalculatorCreator | |
| CIAMover | |
| CIdentifyCDRClusters | |
| CIntegral | |
| CInteractionGraphPerformanceBenchmark | |
| CKernel | |
| CLigandBaseProtocol | |
| CLigandDockBench | |
| CLigandDockBenchmark | |
| CLigandDockScriptBenchmark | |
| CLigandRepackMinimizeProtocol | |
| Cmap_wrapper | |
| CMinimize | |
| CMinimizerBenchmark | |
| CMover | |
| CmyMC | |
| CMyScoreMover | |
| CNBuriedUnsatsCalcultor | |
| CNBuriedUnsatsCalcultorCreator | |
| CNCMinimize | |
| CNPDPropCalculator | |
| CNPDPropCalculatorCreator | |
| CONE_CLASS_Q | |
| COOO | |
| COopDesignMover | |
| COptionCollectionBenchmark | |
| CPackingAngle | |
| CPDB_IOBenchmark | |
| Cpep_coord_cst | |
| CPeptoidDesignMover | |
| CPerformanceBenchmark | |
| CPhProtocol | |
| CPointers_and_References | |
| CPosePyObserver | |
| CPosePyObserver2 | |
| CQMatrix | |
| CRecursiveASTVisitor | |
| CResidueTypeBenchmark | |
| CRmsfMover | |
| CScoreAnalyticEtableBenchmark | |
| CScoreBenchmark | |
| CScoreEachBenchmark | |
| CScoreFragInfo | |
| CScoreFragmentSetMover | |
| CShearMoverBenchmark | |
| CSmallMoverBenchmark | |
| CSolutionRescoreMover | |
| ►CSolver | |
| CSolutionInfo | |
| CSolver_NU | |
| CSpecT | |
| Csupercharge | Adds charged residues to a protein surface |
| CSVC_Q | |
| Csvm_model | |
| Csvm_node | |
| Csvm_parameter | |
| Csvm_problem | |
| CSVR_Q | |
| CTkFrame | |
| Ctype | |
| CUBQ_E2Mover | |
| CUBQ_GTPase_disulfide_Mover | |
| CUBQ_GTPaseMover | |
| CViewMembraneProteinMover | Quick Container Mover: Visualize Membrane Protein Using the PyMol Viewer |
| CW128_T | |
| Cwrapper | |
| CWrapper_PosePyObserver | |
| CXMLParseBenchmark | |
| Czinc1_homodimer_design | |
| Czinc1_homodimer_setup | |
| Czinc2_homodimer_design | |
| Czinc2_homodimer_setup | |
1.8.7
