- s -
- sampleCount()
: gmx::AnalysisDataAverageModule
, gmx::AnalysisDataFrameAverager
- SasaModuleData()
: gmx::analysismodules::anonymous_namespace{sasa.cpp}::SasaModuleData
- scaleAll()
: gmx::AbstractAverageHistogram
- scaleAllByVector()
: gmx::AbstractAverageHistogram
- scaleSingle()
: gmx::AbstractAverageHistogram
- scoped_cptr()
: gmx::scoped_cptr< T, D >
- seed()
: gmx::ThreeFry2x64General< rounds, internalCounterBits >
- selectDataSet()
: gmx::AnalysisDataHandle
, gmx::AnalysisDataStorageFrame
- selected()
: gmx::SelectionPosition
- Selection()
: gmx::Selection
- SelectionCollection()
: gmx::SelectionCollection
- selectionCollection()
: gmx::AnalysisDataPlotSettings
- SelectionCompiler()
: gmx::SelectionCompiler
- SelectionData()
: gmx::internal::SelectionData
- SelectionFileOption()
: gmx::SelectionFileOption
- SelectionFileOptionInfo()
: gmx::SelectionFileOptionInfo
- SelectionFileOptionStorage()
: gmx::SelectionFileOptionStorage
- SelectionOption()
: gmx::SelectionOption
- SelectionOptionBehavior()
: gmx::SelectionOptionBehavior
- SelectionOptionInfo()
: gmx::SelectionOptionInfo
- SelectionOptionManager()
: gmx::SelectionOptionManager
- SelectionOptionStorage()
: gmx::SelectionOptionStorage
- SelectionParserSymbolIterator()
: gmx::SelectionParserSymbolIterator
- SelectionParserSymbolTable()
: gmx::SelectionParserSymbolTable
- SelectionPosition()
: gmx::SelectionPosition
- SelectionRequest()
: gmx::SelectionOptionManager::Impl::SelectionRequest
- selectionText()
: gmx::Selection
, gmx::internal::SelectionData
- SelectionTreeElement()
: gmx::SelectionTreeElement
- selectSingleFromArray()
: gmx::AnalysisNeighborhoodPositions
- SelelemTemporaryValueAssigner()
: anonymous_namespace{evaluate.cpp}::SelelemTemporaryValueAssigner
- set()
: gmx::FlagsTemplate< FlagType >
- setAbsTol()
: gmx::test::SimdBaseTest
- setAcceptBooleanNoPrefix()
: gmx::OptionsAssigner
- setAllowedValueCount()
: gmx::SelectionOptionStorage
- setAverageDataSets()
: gmx::AnalysisDataAverageModule
- setCalculateAtomArea()
: gmx::SurfaceAreaCalculator
- setCalculateSurfaceDots()
: gmx::SurfaceAreaCalculator
- setCalculateVolume()
: gmx::SurfaceAreaCalculator
- setColumnCount()
: gmx::AbstractAnalysisData
, gmx::AnalysisData
, gmx::AbstractAnalysisArrayData
, gmx::AnalysisDataFrameLocalData< ValueType >
, gmx::AnalysisDataFrameAverager
, gmx::test::AnalysisDataTestInput
- setColumnFirstLineOffset()
: gmx::TextTableFormatter
- setContinuationChar()
: gmx::TextLineWrapperSettings
- setCumulative()
: gmx::AnalysisDataLifetimeModule
- setCutoff()
: gmx::AnalysisNeighborhood
- setDataSetCount()
: gmx::AbstractAnalysisData
, gmx::AnalysisData
, gmx::AnalysisDataFrameLocalData< ValueType >
- setDatasetTolerance()
: gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
- setDebugLevel()
: gmx::SelectionCollection
- setDefaultNiceLevel()
: gmx::CommandLineModuleSettings
- setDefaultTolerance()
: gmx::test::TestReferenceChecker
- setDefaultValue()
: gmx::OptionStorageTemplate< T >
- setDefaultValueIfSet()
: gmx::OptionStorageTemplate< T >
- setDescription()
: gmx::AbstractOption
- setDisplayName()
: gmx::CommandLineProgramContext
- setDotCount()
: gmx::SurfaceAreaCalculator
- setDynamicMask()
: gmx::SelectionOptionInfo
- setError()
: gmx::AnalysisDataValue
- setErrorsAsSeparateColumn()
: gmx::AbstractPlotModule
- setEvaluateForces()
: gmx::Selection
, gmx::SelectionOptionInfo
- setEvaluateVelocities()
: gmx::Selection
, gmx::SelectionOptionInfo
- setExpectedDisplayName()
: gmx::test::MockModule
- setFileName()
: gmx::AbstractPlotModule
, gmx::analysismodules::anonymous_namespace{select.cpp}::IndexFileWriterModule
- setFirstColumnIndent()
: gmx::TextTableFormatter
- setFirstLineIndent()
: gmx::TextLineWrapperSettings
- setFlag()
: gmx::AbstractOption
, gmx::AbstractOptionStorage
, gmx::TrajectoryAnalysisSettings
- setFlags()
: gmx::internal::SelectionData
, gmx::TrajectoryAnalysisSettings
- setFoldLastColumnToNextLine()
: gmx::TextTableFormatter
- setFrameFlags()
: gmx::TrajectoryAnalysisSettings
- setGlobalOutputTempDirectory()
: gmx::test::TestFileManager
- setHelpText()
: gmx::CommandLineHelpWriter
, gmx::ICommandLineOptionsModuleSettings
, gmx::TrajectoryAnalysisSettings
- setIndent()
: gmx::TextLineWrapperSettings
- setIndexGroups()
: gmx::SelectionCollection
- setInfo()
: gmx::GromacsException
- setInputDataDirectory()
: gmx::test::TestFileManager
- setInputFile()
: gmx::test::CommandLineTestBase
- setInputFileContents()
: gmx::test::CommandLineTestHelper
, gmx::test::CommandLineTestBase
- setInputLines()
: gmx::test::InteractiveTestHelper
- setInputRedirector()
: gmx::FileNameOptionManager
- setKeepFinalSpaces()
: gmx::TextLineWrapperSettings
- setKnownIssues()
: gmx::CommandLineHelpWriter
- setLastNewline()
: gmx::test::InteractiveTestHelper
- setLegend()
: gmx::AbstractPlotModule
- setLineLength()
: gmx::TextLineWrapperSettings
- setMaxTime()
: gmx::AnalysisDataDisplacementModule
- setMaxValueCount()
: gmx::AbstractOptionStorage
- setMinValueCount()
: gmx::AbstractOptionStorage
- setMode()
: gmx::AnalysisNeighborhood
- setModuleDisplayName()
: gmx::CommandLineHelpContext
- setModuleOverride()
: gmx::CommandLineHelpModule
- setMSDHistogram()
: gmx::AnalysisDataDisplacementModule
- setMultipoint()
: gmx::AbstractAnalysisData
, gmx::AnalysisData
- setName()
: gmx::SelectionTreeElement
- setOmitX()
: gmx::AbstractPlotModule
- setOnlyAtoms()
: gmx::SelectionOptionInfo
- setOnlyStatic()
: gmx::SelectionOptionInfo
- setOptionsModuleSettings()
: gmx::TrajectoryAnalysisSettings
- setOriginalId()
: gmx::Selection
- setOutputFile()
: gmx::test::CommandLineTestHelper
, gmx::test::CommandLineTestBase
- setOutputPosType()
: gmx::SelectionCollection
- setOutputRedirector()
: gmx::CommandLineHelpModule
, gmx::CommandLineModuleManager
- setOutputTempDirectory()
: gmx::test::TestFileManager
- setPBC()
: gmx::TrajectoryAnalysisSettings
- setPlainOutput()
: gmx::AbstractPlotModule
- setPoint()
: gmx::AnalysisDataHandle
- setPoints()
: gmx::AnalysisDataHandle
- setQuiet()
: gmx::CommandLineModuleManager
- setRadii()
: gmx::SurfaceAreaCalculator
- setRange()
: gmx::test::SimdBaseTest
- setReferencePosType()
: gmx::SelectionCollection
- setReplacement()
: gmx::HelpWriterContext
- setRmPBC()
: gmx::TrajectoryAnalysisSettings
- setRowCount()
: gmx::AbstractAnalysisArrayData
- setScaleFactor()
: gmx::DoubleOptionInfo
, gmx::FloatOptionInfo
, gmx::DoubleOptionStorage
, gmx::FloatOptionStorage
- setSearchPathFromEnv()
: gmx::DataFileFinder
- setSelectionCollection()
: gmx::AnalysisDataPlotSettings
- setSelectionFlag()
: gmx::SelectionOptionStorage
- setSettings()
: gmx::AbstractPlotModule
- setShowHidden()
: gmx::CommandLineHelpContext
, gmx::CommandLineHelpModule
, gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::OptionsFilter
- setSignals()
: gmx::SimulationSignaller
- setSingleModule()
: gmx::CommandLineModuleManager
- setStoreIsSet()
: gmx::AbstractOption
- setSubtitle()
: gmx::AbstractPlotModule
- setTimeUnit()
: gmx::AnalysisDataPlotSettings
, gmx::TimeUnitManager
, gmx::TimeUnitBehavior
- setTimeUnitFromEnvironment()
: gmx::TimeUnitBehavior
- setTimeUnitStore()
: gmx::TimeUnitBehavior
- settings()
: gmx::TextLineWrapper
, gmx::AnalysisDataBinAverageModule
, gmx::AbstractAverageHistogram
, gmx::AnalysisDataSimpleHistogramModule
, gmx::AnalysisDataWeightedHistogramModule
, gmx::anonymous_namespace{helpwritercontext.cpp}::IWrapper
, gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToString
, gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToVector
- setTitle()
: gmx::AbstractPlotModule
- SettleTest()
: gmx::test::SettleTest
- setTopology()
: gmx::PositionCalculationCollection
, gmx::SelectionCollection
, gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
- setTopologyExclusions()
: gmx::AnalysisNeighborhood
- setTrajectory()
: gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
- setUlpTol()
: gmx::test::SimdBaseTest
- SetUp()
: anonymous_namespace{shake.cpp}::ShakeTest
- setupArrayData()
: gmx::test::AnalysisDataTestFixture
- setupDataObject()
: gmx::test::AnalysisDataTestFixture
- setupGrompp()
: gmx::test::BondedInteractionsTest
- setupMdrun()
: gmx::test::BondedInteractionsTest
- setValue()
: gmx::AnalysisDataValue
, gmx::AnalysisDataStorageFrame
- setValueCount()
: gmx::SelectionOptionInfo
, gmx::AbstractOption
- setVector()
: gmx::AbstractOption
- setWriteMask()
: gmx::AnalysisDataVectorPlotModule
- setWriteNorm()
: gmx::AnalysisDataVectorPlotModule
- setWriteX()
: gmx::AnalysisDataVectorPlotModule
- setWriteY()
: gmx::AnalysisDataVectorPlotModule
- setWriteZ()
: gmx::AnalysisDataVectorPlotModule
- setXAxis()
: gmx::AbstractAnalysisArrayData
- setXAxisIsTime()
: gmx::AbstractPlotModule
- setXAxisValue()
: gmx::AbstractAnalysisArrayData
- setXFormat()
: gmx::AbstractPlotModule
- setXLabel()
: gmx::AbstractPlotModule
- setXYMode()
: gmx::AnalysisNeighborhood
- setYFormat()
: gmx::AbstractPlotModule
- setYLabel()
: gmx::AbstractPlotModule
- SharedState()
: gmx::HelpWriterContext::Impl::SharedState
- shellCompletionWriter()
: gmx::CommandLineHelpContext
- shortDescription()
: gmx::test::MockModule
, gmx::CommandLineHelpModule
, gmx::ICommandLineModule
, gmx::anonymous_namespace{cmdlinemodulemanager.cpp}::CMainCommandLineModule
, anonymous_namespace{legacymodules.cpp}::ObsoleteToolModule
- shouldBackup()
: gmx::CommandLineCommonOptionsHolder
- shouldBeQuiet()
: gmx::CommandLineCommonOptionsHolder
- shouldIgnore()
: gmx::test::TestReferenceChecker::Impl
- shouldIgnoreActualModule()
: gmx::CommandLineCommonOptionsHolder
- shouldNotifyImmediately()
: gmx::internal::AnalysisDataStorageImpl
- shouldShowHelp()
: gmx::CommandLineCommonOptionsHolder
- shouldShowHidden()
: gmx::CommandLineCommonOptionsHolder
- showHidden()
: gmx::CommandLineHelpContext
- signalInterSim()
: gmx::SimulationSignaller
- SignalTest()
: gmx::test::SignalTest
- signsDiffer()
: gmx::test::FloatingPointDifference
- Simd4DBool()
: gmx::Simd4DBool
- Simd4Double()
: gmx::Simd4Double
- Simd4FBool()
: gmx::Simd4FBool
- Simd4Float()
: gmx::Simd4Float
- SimdBaseTest()
: gmx::test::SimdBaseTest
- SimdDBool()
: gmx::SimdDBool
- SimdDIBool()
: gmx::SimdDIBool
- SimdDInt32()
: gmx::SimdDInt32
- SimdDouble()
: gmx::SimdDouble
- SimdFBool()
: gmx::SimdFBool
- SimdFIBool()
: gmx::SimdFIBool
- SimdFInt32()
: gmx::SimdFInt32
- SimdFloat()
: gmx::SimdFloat
- SimulationInstabilityError()
: gmx::SimulationInstabilityError
- SimulationRunner()
: gmx::test::SimulationRunner
- SimulationSignal()
: gmx::SimulationSignal
- SimulationSignaller()
: gmx::SimulationSignaller
- size()
: gmx::ConstArrayRef< T >
, gmx::test::AnalysisDataTestInputPointSet
, gmx::ArrayRef< T >
- skipRemainingPairsForTestPosition()
: gmx::AnalysisNeighborhoodPairSearch
- skipUnknown()
: gmx::CommandLineParser
- standardDeviation()
: gmx::AnalysisDataAverageModule
- standardError()
: gmx::TextOutputFile
- standardOutput()
: gmx::test::TestFileOutputRedirector
, gmx::IFileOutputRedirector
, gmx::anonymous_namespace{fileredirector.cpp}::DefaultOutputRedirector
, gmx::TextOutputFile
- start()
: gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::SynopsisFormatter
, gmx::OptionsAssigner
, gmx::AnalysisHistogramSettingsInitializer
- startContext()
: gmx::MessageStringCollector
- startData()
: gmx::AnalysisData
- startDataStorage()
: gmx::AnalysisDataStorage
- startFormatting()
: gmx::TextTableFormatter::Impl::ColumnData
- startFrame()
: gmx::AnalysisDataStorage
, gmx::internal::AnalysisDataStorageFrameData
, gmx::AnalysisDataStorage
, gmx::AnalysisDataHandle
- startFrames()
: gmx::TrajectoryAnalysisModule
, gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance
, gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf
, gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa
- startModuleExport()
: gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::IHelpExport
, gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportCompletion
, gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText
- startModuleGroupExport()
: gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText
, gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportCompletion
, gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::IHelpExport
- startOption()
: gmx::OptionsAssigner
- startPairSearch()
: gmx::AnalysisNeighborhoodSearch
- startParallelDataStorage()
: gmx::AnalysisDataStorage
- startReferenceData()
: gmx::test::MockAnalysisDataModule::Impl
- startReferenceFrame()
: gmx::test::MockAnalysisDataModule::Impl
- startSection()
: gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::OptionsListFormatter
- startSet()
: gmx::AbstractOptionStorage
- startSource()
: gmx::AbstractOptionStorage
, gmx::internal::OptionsImpl
- startSubSection()
: gmx::OptionsAssigner
- startupInfoFile()
: gmx::CommandLineCommonOptionsHolder
- StaticAverageHistogram()
: gmx::anonymous_namespace{histogram.cpp}::StaticAverageHistogram
- StaticDataFrameHeaderChecker()
: gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataFrameHeaderChecker
- StaticDataPointsChecker()
: gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsChecker
- StaticDataPointsStorageChecker()
: gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsStorageChecker
- stddev()
: gmx::NormalDistribution< RealType >
, gmx::TabulatedNormalDistribution< RealType, tableBits >
, gmx::NormalDistribution< RealType >::param_type
, gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type
- stepping()
: gmx::CpuInfo
- storageImpl()
: gmx::internal::AnalysisDataStorageFrameData
- store()
: gmx::OptionTemplate< T, U >
- storeAll()
: gmx::internal::AnalysisDataStorageImpl
- storeCount()
: gmx::OptionTemplate< T, U >
- storeIsSet()
: gmx::OptionTemplate< T, U >
- storeVector()
: gmx::OptionTemplate< T, U >
- StringFormatter()
: gmx::StringFormatter
- StringInputStream()
: gmx::StringInputStream
- StringKeywordMatchItem()
: anonymous_namespace{sm_keywords.cpp}::StringKeywordMatchItem
- StringOption()
: gmx::StringOption
- StringOptionInfo()
: gmx::StringOptionInfo
- StringOptionStorage()
: gmx::StringOptionStorage
- stringValue()
: gmx::SelectionParserValue
- substituteMarkupAndWrapToString()
: gmx::HelpWriterContext
- substituteMarkupAndWrapToVector()
: gmx::HelpWriterContext
- supportLevel()
: gmx::CpuInfo
, gmx::HardwareTopology
- SurfaceAreaCalculator()
: gmx::SurfaceAreaCalculator
- swap()
: gmx::ArrayRef< T >
, gmx::ConstArrayRef< T >
- SynopsisFormatter()
: gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::SynopsisFormatter