Gromacs  2016.4
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Class Hierarchy

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This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
oCgmx::ArrayRef< ValueType >
oCgmx::ConstArrayRef< AnalysisDataValue >
oCgmx::ConstArrayRef< const char * >
oCgmx::ConstArrayRef< real >
oCgmx::FlagsTemplate< Flag >
oCgmx::FlagsTemplate< OptionFlag >
oCgmx::AbstractAnalysisDataAbstract base class for all objects that provide data
oCgmx::AbstractOptionAbstract base class for specifying option properties
oCgmx::AbstractOptionStorageAbstract base class for converting, validating, and storing option values
oCgmx::AlignedAllocator< T >Aligned memory allocator
oCgmx::AlignedAllocator< T >::rebind< U >Standard-required typedef to use allocator with different class
oCgmx::AnalysisDataFrameHeaderValue type for storing frame-level information for analysis data
oCgmx::AnalysisDataFrameRefValue type wrapper for non-mutable access to a data frame
oCgmx::AnalysisDataHandleHandle for inserting data into AnalysisData
oCgmx::AnalysisDataModuleManagerEncapsulates handling of data modules attached to AbstractAnalysisData
oCgmx::AnalysisDataParallelOptionsParallelization options for analysis data objects
oCgmx::AnalysisDataPlotSettingsCommon settings for data plots
oCgmx::AnalysisDataPointSetRefValue type wrapper for non-mutable access to a set of data column values
oCgmx::AnalysisDataStorageHelper class that implements storage of data
oCgmx::AnalysisDataStorageFrameAllows assigning values for a data frame in AnalysisDataStorage
oCgmx::AnalysisDataValueValue type for representing a single value in analysis data objects
oCgmx::AnalysisHistogramSettingsContains parameters that specify histogram bin locations
oCgmx::AnalysisHistogramSettingsInitializerProvides "named parameter" idiom for constructing histograms
oCgmx::AnalysisNeighborhoodNeighborhood searching for analysis tools
oCgmx::AnalysisNeighborhoodPairValue type to represent a pair of positions found in neighborhood searching
oCgmx::AnalysisNeighborhoodPairSearchInitialized neighborhood pair search with a fixed set of positions
oCgmx::AnalysisNeighborhoodPositionsInput positions for neighborhood searching
oCgmx::AnalysisNeighborhoodSearchInitialized neighborhood search with a fixed set of reference positions
oCgmx::ArrayRef< T >STL-like container for an interface to a C array (or part of a std::vector)
oCgmx::BasicVector< ValueType >C++ class for 3D vectors
oCgmx::BinaryInformationSettingsSettings for printBinaryInformation()
oCgmx::CommandLineHelpContextContext information for writing out command-line help
oCgmx::CommandLineHelpWriterWrites help information for Options
oCgmx::CommandLineModuleGroupHandle to add content to a group added with CommandLineModuleManager::addModuleGroup()
oCgmx::CommandLineModuleManagerImplements a wrapper command-line interface for multiple modules
oCgmx::CommandLineModuleSettingsSettings to pass information between a module and the general runner
oCgmx::CommandLineParserImplements command-line parsing for Options objects
oCgmx::ConstArrayRef< T >STL-like container for non-mutable interface to a C array (or part of a std::vector)
oCgmx::CpuInfoDetect CPU capabilities and basic logical processor info
oCgmx::CpuInfo::LogicalProcessorEntry with basic information for a single logical processor
oCgmx::DataFileFinderSearches data files from a set of paths
oCgmx::DataFileInfoInformation about a data file found by DataFileFinder::enumerateFiles()
oCgmx::DataFileOptionsSearch parameters for DataFileFinder
oCgmx::DirectoryEnumeratorLists files in a directory
oCgmx::EmptyArrayRefTag type to initialize empty array references
oCgmx::ExceptionInfo< Tag, T >Stores additional context information for exceptions
oCgmx::ExceptionInitializerProvides information for Gromacs exception constructors
oCgmx::ExponentialDistribution< RealType >Exponential distribution
oCgmx::ExponentialDistribution< RealType >::param_typeExponential distribution parameters
oCgmx::FlagsTemplate< FlagType >Template class for typesafe handling of combination of flags
oCgmx::GammaDistribution< RealType >Gamma distribution
oCgmx::GammaDistribution< RealType >::param_typeGamma distribution parameters
oCgmx::GlobalCommandLineHelpContextHelper for passing CommandLineHelpContext into parse_common_args()
oCgmx::HardwareTopologyInformation about sockets, cores, threads, numa, caches
oCgmx::HardwareTopology::CacheInformation about a single cache level
oCgmx::HardwareTopology::CoreInformation about a single core in a socket
oCgmx::HardwareTopology::DeviceInformation about a single PCI device
oCgmx::HardwareTopology::HWThreadInformation about a single hardware thread in a core
oCgmx::HardwareTopology::LogicalProcessorInformation about socket, core and hwthread for a logical processor
oCgmx::HardwareTopology::MachineHardware topology information about the entire machine
oCgmx::HardwareTopology::NumaInformation about a single numa node
oCgmx::HardwareTopology::NumaNodeInformation about each numa node in system
oCgmx::HardwareTopology::SocketInformation about a single socket in the system
oCgmx::HelpLinksHyperlink data for writing out help
oCgmx::HelpManagerHelper for providing interactive online help
oCgmx::HelpWriterContextContext information for writing out help
oCgmx::IAnalysisDataModuleInterface for a module that gets notified whenever data is added
oCgmx::ICommandLineModuleModule that can be run from command line using CommandLineModuleManager
oCgmx::ICommandLineOptionsModuleModule that can be run from a command line and uses gmx::Options for argument processing
oCgmx::ICommandLineOptionsModuleSettingsSettings to pass information between a CommandLineOptionsModule and generic code that runs it
oCgmx::IdentityFormatterFunction object to implement the same interface as StringFormatter to use with strings that should not be formatted further
oCgmx::IExecutableEnvironmentAllows customization of the way various directories are found by CommandLineProgramContext
oCgmx::IFileInputRedirectorAllows overriding file existence checks from code that supports it
oCgmx::IFileOutputRedirectorAllows capturing stdout and file output from code that supports it
oCgmx::IHelpTopicProvides a single online help topic
oCgmx::InstallationPrefixInfoProvides information about installation prefix (see IProgramContext::installationPrefix())
oCgmx::IOptionManagerBase class for option managers
oCgmx::IOptionsBehaviorInterface to provide extension points for options parsing
oCgmx::IOptionsContainerInterface for adding input options
oCgmx::IProgramContextProvides context information about the program that is calling the library
oCgmx::ITopologyProviderProvides topology information to SelectionOptionBehavior
oCgmx::MessageStringCollectorHelper class for collecting message strings, optionally with context
oCgmx::MessageStringContextConvenience class for creating a message context
oCgmx::no_delete< T >Deleter for std::shared_ptr that does nothing
oCgmx::NormalDistribution< RealType >Normal distribution
oCgmx::NormalDistribution< RealType >::param_typeNormal distribution parameters
oCgmx::OptionInfoGives information and allows modifications to an option after creation
oCgmx::OptionManagerContainerContainer to keep managers added with Options::addManager() and pass them to options
oCgmx::OptionsAssignerDecorator class for assigning values to Options
oCgmx::OptionsBehaviorCollectionContainer for IOptionsBehavior objects
oCgmx::OptionsIteratorDecorator class for visiting options in a Options object
oCgmx::OptionsModifyingIteratorDecorator class for visiting options in a Options object, allowing changes
oCgmx::OptionsModifyingVisitorPure interface for visiting options in a Options object, allowing modifications
oCgmx::OptionsVisitorPure interface for visiting options in a Options object
oCgmx::PrivateImplPointer< Impl >Helper class to manage a pointer to a private implementation class
oCgmx::RegexRepresents a regular expression
oCgmx::scoped_cptr< T, D >Stripped-down version of scoped_ptr that uses sfree() or custom deleter
oCgmx::SelectionProvides access to a single selection
oCgmx::SelectionCollectionCollection of selections
oCgmx::SelectionPositionProvides access to information about a single selected position
oCgmx::Simd4DBoolSIMD4 variable type to use for logical comparisons on doubles
oCgmx::Simd4DoubleSIMD4 double type
oCgmx::Simd4FBoolSIMD4 variable type to use for logical comparisons on floats
oCgmx::Simd4FloatSIMD4 float type
oCgmx::SimdDBoolBoolean type for double SIMD data
oCgmx::SimdDIBoolBoolean type for integer datatypes corresponding to double SIMD
oCgmx::SimdDInt32Integer SIMD variable type to use for conversions to/from double
oCgmx::SimdDoubleDouble SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1
oCgmx::SimdFBoolBoolean type for float SIMD data
oCgmx::SimdFIBoolBoolean type for integer datatypes corresponding to float SIMD
oCgmx::SimdFInt32Integer SIMD variable type to use for conversions to/from float
oCgmx::SimdFloatFloat SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1
oCgmx::SimdLoadDProxyInternalProxy object to enable load() for SIMD and double types
oCgmx::SimdLoadFProxyInternalProxy object to enable load() for SIMD and float types
oCgmx::SimdLoadIProxyInternalProxy object load() for SimdFInt32, SImdDInt32, and int32
oCgmx::SimdLoadUDProxyInternalProxy object to enable loadU() for SIMD and double types
oCgmx::SimdLoadUFProxyInternalProxy object to enable loadU() for SIMD and float types
oCgmx::SimdLoadUIProxyInternalProxy object - loadU() for SimdFInt32, SImdDInt32, and int32
oCgmx::SimdSetZeroProxyInternalProxy object to enable setZero() for SIMD and real types
oCgmx::StaticLog2< n >Evaluate log2(n) for integer n statically at compile time
oCgmx::StaticLog2< 0 >Specialization of StaticLog2<n> for n==0
oCgmx::StaticLog2< 1 >Specialization of StaticLog2<n> for n==1
oCgmx::StringFormatterFunction object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms
oCgmx::TabulatedNormalDistribution< RealType, tableBits >Tabulated normal random distribution
oCgmx::TabulatedNormalDistribution< RealType, tableBits >::param_typeNormal distribution parameter class (mean and stddev)
oCgmx::test::AnalysisDataTestFixtureTest fixture for AbstractAnalysisData testing
oCgmx::test::AnalysisDataTestInputRepresents static input data for AbstractAnalysisData tests
oCgmx::test::AnalysisDataTestInputFrameRepresents a single frame in AnalysisDataTestInput structure
oCgmx::test::AnalysisDataTestInputPointSetRepresents a single set of points in AnalysisDataTestInputFrame structure
oCgmx::test::CommandLineHelper class for tests that need to construct command lines
oCgmx::test::CommandLineTestBaseTest fixture for tests that call a single command-line program with input/output files
oCgmx::test::CommandLineTestHelperHelper class for tests that construct command lines that need to reference existing files
oCgmx::test::FloatingPointDifferenceComputes and represents a floating-point difference value
oCgmx::test::FloatingPointToleranceSpecifies a floating-point comparison tolerance and checks whether a difference is within the tolerance
oCgmx::test::IntegrationTestFixtureTest fixture for integration tests
oCgmx::test::InteractiveTestHelperHelper class for testing interactive sessions
oCgmx::test::ITextBlockMatcherRepresents a text matcher, matching text stream contents against reference data
oCgmx::test::ITextBlockMatcherSettingsRepresents a factory for creating a text matcher
oCgmx::test::MdrunComparisonFixtureDeclares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun
oCgmx::test::StringTestBaseTest fixture for tests that check string formatting
oCgmx::test::TestFileManagerHelper for tests that need input and output files
oCgmx::test::TestOptionsProviderProvides additional options for the test executable
oCgmx::test::TestReferenceCheckerHandles comparison to test reference data
oCgmx::test::TestReferenceDataHandles creation of and comparison to test reference data
oCgmx::TextInputStreamInterface for reading text
oCgmx::TextLineWrapperWraps lines to a predefined length
oCgmx::TextLineWrapperSettingsStores settings for line wrapping
oCgmx::TextOutputStreamInterface for writing text
oCgmx::TextReaderReads text from a TextInputStream
oCgmx::TextTableFormatterFormats rows of a table for text output
oCgmx::TextWriterWrites text into a TextOutputStream
oCgmx::ThreeFry2x64General< rounds, internalCounterBits >General implementation class for ThreeFry counter-based random engines
oCgmx::TimeUnitManagerProvides common functionality for time unit conversions
oCgmx::TopologyInformationTopology information passed to a trajectory analysis module
oCgmx::TrajectoryAnalysisCommandLineRunnerRunner for command-line trajectory analysis tools
oCgmx::TrajectoryAnalysisModuleBase class for trajectory analysis modules
oCgmx::TrajectoryAnalysisModuleDataBase class for thread-local data storage during trajectory analysis
oCgmx::TrajectoryAnalysisSettingsTrajectory analysis module configuration object
oCgmx::UniformIntDistribution< IntType >Uniform integer distribution
oCgmx::UniformIntDistribution< IntType >::param_typeUniform int distribution parameters
oCgmx::UniformRealDistribution< RealType >Uniform real distribution
oCgmx::UniformRealDistribution< RealType >::param_typeUniform real distribution parameters
oCgmx_ana_index_tStores a single index group
oCgmx_ana_indexmap_tData structure for calculating index group mappings
oCgmx_ana_pos_tStores a set of positions together with their origins
oCgmx_ga2la_tStructure for all global to local mapping information
oCgmx_laa_tStructure for the local atom info for a plain list
oCgmx_lal_tStructure for the local atom info for a hash table
oCgmx_sparsematrixSparse matrix storage format
oCgmx::PrivateImplPointer< internal::FileStreamImpl >
oCgmx::PrivateImplPointer< internal::OptionsImpl >
oCgmx::scoped_cptr< ener_file, done_ener_file >
oCgmx::scoped_cptr< gmx_output_env_t, output_env_done >
oCgmx::scoped_cptr< struct warninp, free_warning >
oCgmx::scoped_cptr< t_enxframe, done_enxframe >
oCgmx::scoped_cptr< t_inpfile >
oCgmx::scoped_cptr< t_trxframe, done_trxframe >
oCgmx::scoped_cptr< t_trxstatus, close_trx >
oCstd::exceptionSTL class
oCt_cosinesDeclares inputrec data structure and utilities
oCt_filenmFile name option definition for C code
oCt_mdatomsDeclares mdatom data structure
oCt_pargsCommand-line argument definition for C code
oCt_pbcStructure containing info on periodic boundary conditions
oCgmx::ThreeFry2x64General< 13, internalCounterBits >
\Cgmx::ThreeFry2x64General< 20, internalCounterBits >