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Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
oCgmx::ArrayRef< BoundingBox >
oCgmx::ArrayRef< const AnalysisDataValue >
oCgmx::ArrayRef< const char *const >
oCgmx::ArrayRef< const char >
oCgmx::ArrayRef< const double >
oCgmx::ArrayRef< const float >
oCgmx::ArrayRef< const gmx::BasicVector >
oCgmx::ArrayRef< const int >
oCgmx::ArrayRef< const InteractionList >
oCgmx::ArrayRef< const real >
oCgmx::ArrayRef< const t_filenm >
oCgmx::ArrayRef< const t_iparams >
oCgmx::ArrayRef< gmx::BasicVector >
oCgmx::ArrayRef< gmx::gmx::BasicVector >
oCgmx::ArrayRef< gmx::RVec >
oCgmx::ArrayRef< PpRanks >
oCgmx::ArrayRef< real >
oCgmx::ArrayRef< rvec >
oCgmx::ArrayRef< ValueType >
oCgmx::ArrayRefWithPadding< gmx::BasicVector >
oCgmx::ArrayRefWithPadding< gmx::gmx::BasicVector >
oCAtomIteratorObject that allows looping over all atoms in an mtop
oCAtomPropertiesHolds all the atom property information loaded
oCAtomProxyProxy object returned from AtomIterator
oCAtomRangeRange over all atoms of topology
oCgmx::BasicVector< double >
oCgmx::BasicVector< int >
oCgmx::BasicVector< real >
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCdf_history_tFree-energy sampling history struct
oCgmx::FlagsTemplate< Flag >
oCForceHelperBuffersHelper force buffers for ForceOutputs
oCForeignLambdaTermsAccumulates free-energy foreign lambda energies and dH/dlamba
oCgmx::AbstractAnalysisDataAbstract base class for all objects that provide data
oCgmx::AbstractOptionAbstract base class for specifying option properties
oCgmx::AbstractOptionSectionBase class for specifying option section properties
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::AnalysisDataPlotSettingsCommon settings for data plots
oCgmx::AnalysisDataPointSetRefValue type wrapper for non-mutable access to a set of data column values
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< typename >STL-like interface to a C array of T (or part of a std container of T)
oCgmx::ArrayRefWithPadding< typename >Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses
oCgmx::BasicVector< ValueType >C++ class for 3D vectors
oCgmx::BenchmarkSystemDescription of the system used for benchmarking
oCgmx::BoxDeformationHandleHandle to information about the box
oCgmx::CheckpointData< operation >}
oCgmx::CommandLineHelpWriterWrites help information for Options
oCgmx::CommandLineModuleSettingsSettings to pass information between a module and the general runner
oCgmx::CommandLineParserImplements command-line parsing for Options objects
oCgmx::ConstraintsParamCollection of constraint parameters
oCgmx::ConvertTprInfoDeclares gmx convert-tpr
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::detail::PaddingTraits< T >Traits classes for handling padding for types used with PaddedVector
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::FixedCapacityVector< T, capacity >Vector that behaves likes std::vector but has fixed capacity
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::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::InstallationPrefixInfoProvides information about installation prefix (see IProgramContext::installationPrefix())
oCgmx::InteractiveMDSimulatorBuilder parameter type for InteractiveMD
oCgmx::IonSwappingParameter type for IonSwapping SimulatorBuilder component
oCgmx::IOptionManagerBase class for option managers
oCgmx::IOptionsBehaviorInterface to provide extension points for options parsing
oCgmx::IOptionsContainerInterface for adding input options
oCgmx::IOutputAdapterOutputAdapter class for handling trajectory file flag setting and processing
oCgmx::IProgramContextProvides context information about the program that is calling the library
oCgmx::IRestraintPotentialInterface for Restraint potentials
oCgmx::IsSerializableEnum< T, bool >{
oCgmx::ITopologyProviderProvides topology information to SelectionOptionBehavior
oCgmx::LegacyInputCollection of legacy input information
oCgmx::ListOfLists< typename >A list of lists, optimized for performance
oCgmx::MembedHolderMembed SimulatorBuilder parameter type
oCgmx::MtsLevelSetting for a single level for multiple time step integration
oCgmx::NonbondedBenchmarkInfoDeclares gmx nonbonded-bench
oCgmx::NormalDistribution< RealType >Normal distribution
oCgmx::NormalDistribution< RealType >::param_typeNormal distribution parameters
oCgmx::OptionInfoGives information and allows modifications to an option after creation
oCgmx::OutputRequirementOptionDirectorContainer for the user input values that will be used by the builder to determine which OutputAdapters should/could/will be registered to the coordinate file writer
oCgmx::OutputRequirementsFinalized version of requirements after processing
oCgmx::PaddedVector< T, Allocator >PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS
oCgmx::PotentialPointDataStructure to hold the results of IRestraintPotential::evaluate()
oCgmx::PrivateImplPointer< Impl >Helper class to manage a pointer to a private implementation class
oCgmx::ProfilingCollection of profiling information
oCgmx::Range< typename >Defines a range of integer numbers and accompanying operations
oCgmx::Range< typename >::iteratorAn iterator that loops over a range of integers
oCgmx::RangePartitioningDivision of a range of indices into consecutive blocks
oCgmx::SelectionProvides access to a single selection
oCgmx::SelectionCollectionCollection of selections
oCgmx::SelectionPositionProvides access to information about a single selected position
oCgmx::SelectionTopologyPropertiesDescribes topology properties required for selection evaluation
oCgmx::SimulationSignalPOD-style object used by mdrun ranks to set and receive signals within and between simulations
oCgmx::SimulationSignallerObject used by mdrun ranks to signal to each other at this step
oCgmx::SimulatorConfigSimulation configuation settings
oCgmx::SimulatorEnvCollection of environmental information for a simulation
oCgmx::SimulatorStateDataData for a specific simulation state
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::TextLineWrapperWraps lines to a predefined length
oCgmx::TextLineWrapperSettingsStores settings for line wrapping
oCgmx::ThreeFry2x64General< rounds, internalCounterBits >General implementation class for ThreeFry counter-based random engines
oCgmx::TimeUnitManagerProvides common functionality for time unit conversions
oCgmx::TopologyDataCollection of handles to topology information
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::TrajectoryFileOpenerLow level method to take care of only file opening and closing
oCgmx::TrajectoryFrameWriterWrites coordinate frames to a sink, e.g. a trajectory file
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_cache_protect_tCache-line protection buffer
oCgmx_enerdata_tStruct for accumulating all potential energy terms and some kinetic energy terms
oCgmx_ffparams_tStruct that holds all force field parameters for the simulated system
oCgmx_localtop_tThe fully written out topology for a domain over its lifetime
oCgmx_molblock_tBlock of molecules of the same type, used in gmx_mtop_t
oCgmx_moltype_tMolecules type data: atoms, interactions and exclusions
oCgmx_sparsematrixSparse matrix storage format
oCInteractionListHandleType for returning a list of InteractionList references
oCgmx::ListOfLists< int >
oCMoleculeBlockIndicesIndices for a gmx_molblock_t, derived from other gmx_mtop_t contents
oCNbnxm::Grid::DimensionsThe physical dimensions of a grid
oCnbnxn_cj4_tFour-way j-cluster lists
oCnbnxn_cj_tThis is the actual cluster-pair list j-entry
oCnbnxn_cycle_tLocal cycle count struct for profiling
oCnbnxn_excl_tStruct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist
oCnbnxn_im_ei_tInteraction data for a j-group for one warp
oCnbnxn_sciGrouped pair-list i-unit
oCNbnxnPairlistCpuCluster pairlist type for use on CPUs
oCNbnxnPairlistCpuWorkWorking data for the actual i-supercell during pair search
oCNbnxnPairlistCpuWork::IClusterDataStruct for storing coordinats and bounding box for an i-entry during search
oCgmx::PaddedVector< gmx::BasicVector >
oCgmx::PaddedVector< gmx::gmx::BasicVector >
oCgmx::PaddedVector< gmx::RVec >
oCgmx::PaddedVector< real >
oCgmx::PaddedVector< RVec >
oCPairlistSetsContains sets of pairlists
oCPairSearchMain pair-search struct, contains the grid(s), not the pair-list(s)
oCPairsearchWorkThread-local work struct, contains working data for Grid
oCPartialDeserializedTprFileContains the partly deserialized contents of a TPR file
oCPbcAiucCompact and ordered version of the PBC matrix
oCgmx::PrivateImplPointer< internal::FileStreamImpl >
oCgmx::PrivateImplPointer< internal::KeyValueTreeTransformerImpl >
oCgmx::PrivateImplPointer< internal::OptionsImpl >
oCgmx::Range< int >
oCSimulationGroupsContains the simulation atom groups
oCSimulationInputHandleOwning handle to a SimulationInput object
oCstd::exceptionSTL class
oCStringTableA class to store strings for lookup
oCStringTableEntryHelper class to access members in StringTable
oCt_filenmFile name option definition for C code
oCt_mappingMaps an XPM element to an RGB color and a string description
oCt_matrixA matrix of integers, plus supporting values, such as used in XPM output
oCt_mdatomsDeclares mdatom data structure
oCt_pargsCommand-line argument definition for C code
oCt_pbcStructure containing info on periodic boundary conditions
oCt_stateThe microstate of the system
oCt_xpmelmtModels an XPM element
oCgmx::ThreeFry2x64General< 13, internalCounterBits >
\Cgmx::ThreeFry2x64General< 20, internalCounterBits >