- a -

• A3MToCS() : HHblits
• A3MToProfile() : HHblits
• About() : InitMenuBar
• accept() : FileTypeDialog
• Acquire() : AdminRights
• Activate() : Shader , Tool
• ActivateOverlay() : OverlayManager
• ActivateTool() : ToolBar
• ActiveNodesChanged() : SceneWin , InspectorWidget
• ActiveToolChanged() : GLWin , ToolManager
• Add() : StarLoopDesc , StarWriterLoopDesc , PDBize , SpatialOrganizer< ITEM, VEC > , AminoAcidSet , Distances , Dist2Mean , GfxNode , GradientEdit , GradientPresetWidget , GfxNode , PresetEditor , PresetWidget , FastSphereRenderer , Scene , IndexedVertexArray , PointlistOverlay , ToolOptionEnum , WidgetPool , InfoSet , StarLoopDesc , StarWriterLoopDesc
• add_scalar() : ImageStateImpl< T, D >
• AddAction() : ContextMenu , ToolBar
• AddAddRule() : GromacsBlockModifier
• AddAlignedSeq() : MMCifInfoStructRef
• AddAlignment() : SequenceViewer
• AddAllInclusiveBonds() : EntityView
• AddAltAtomPos() : EditorBase , ResidueImpl
• AddAngle() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddAssembly() : LinearIndexer
• AddAtom() : ResidueView , Compound , Diag , GfxView , ChainView , EntityView , BuildingBlock , ResidueView
• AddAtomInternal() : EntityView
• AddAtomRenamingRule() : Forcefield
• AddAuthorsToCitation() : MMCifInfo
• AddBioUnit() : MMCifInfo
• AddBlockModifier() : Forcefield
• AddBond() : Compound , GfxView , AtomView , EntityView , BuildingBlock , Forcefield , GromacsBlockModifier
• AddBuildingBlock() : Forcefield
• AddButton() : ButtonBox
• AddButtonBox() : ButtonBar
• AddCallback() : Progress
• AddChain() : Diag , SequenceViewObject , MMCifInfoBioUnit , EntityView
• AddCharacters() : LinearCharacterContainer
• AddChild() : SceneNode
• AddCitation() : MMCifInfo
• AddCMap() : BuildingBlock , Forcefield , GromacsBlockModifier , Topology
• AddCol() : Table
• AddColumn() : ProfileHandle
• AddCommand() : PythonInterpreterWorker
• AddCompound() : CompoundLib
• AddConstraint() : BuildingBlock , Forcefield
• AddContext() : PythonContext
• AddCyl() : PrimList
• AddCylinder() : IndexedVertexArray
• AddData() : StarWriterLoop
• AddDefault() : InfoHandle
• AddDeleteAtom() : GromacsBlockModifier
• AddDiag() : Diagnostics
• AddDif() : MMCifInfoStructRefSeq
• AddDihedral() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddDisplayMode() : BaseViewObject
• AddDistance() : DistanceMap
• AddDistanceConstraint() : Topology
• AddDockWidget() : MainWindow
• AddEntity() : SequenceViewer
• AddEntityBranchLink() : MMCifInfo
• addError() : _XMLTestResult
• AddExclusion() : BuildingBlock , Topology
• addFailure() : _XMLTestResult
• AddFGMDHBondAcceptor() : Topology
• AddFGMDHBondDonor() : Topology
• AddFrame() : CoordGroupHandle , CoordSource , InMemCoordSource
• AddFrames() : CoordGroupHandle
• AddGradientToInfo() : GradientListModel
• AddHarmonicAngle() : Topology
• AddHarmonicBond() : Topology
• AddHarmonicDistanceRestraint() : Topology
• AddHarmonicImproper() : Topology
• AddHarmonicPositionRestraint() : Topology
• AddHet() : MMCifWriterEntity
• AddHydrogenConstructor() : Forcefield
• AddHydrogenRule() : GromacsHydrogenConstructor
• AddIcoSphere() : IndexedVertexArray
• AddImplicitGenborn() : Forcefield
• AddImproper() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddInt() : Diag
• AddItem() : GradientListModel , PresetEditorListModel , PresetListModel
• AddLabel() : GfxObj
• AddLF() : IsosurfaceGenerator
• AddLine() : PrimList , IndexedVertexArray
• AddLJ() : Forcefield
• AddLJPair() : Forcefield , Topology
• AddMass() : Forcefield
• AddMesh() : PrimList
• AddMMCifEntityIdTr() : MMCifInfo
• AddMMCifPDBChainTr() : MMCifInfo
• AddNode() : Polygon2 , SceneWinModel , PolygonMask
• AddNodeEntryList() : BackboneTrace
• AddObserver() : RenderOptions
• AddOp() : Preset
• AddOperation() : MMCifInfo
• AddOperations() : MMCifInfoBioUnit
• AddOption() : ToolOptionGroup , ToolOptions
• AddOverlay() : DataViewer , OverlayManager
• AddPDBMMCifChainTr() : MMCifInfo
• AddPeriodicDihedral() : Topology
• AddPeriodicImproper() : Topology
• AddPersistentWidget() : MainArea
• AddPoint() : PointCloud , PrimList
• AddPointCloud() : PointCloudManager
• AddPositionConstraint() : Simulation , Topology
• AddPositionConstraints() : Simulation
• AddPositions() : LinearPositionContainer
• AddPresetToInfo() : PresetListModel
• AddProfile() : ContextProfileDB , ProfileDB
• AddQuad() : IndexedVertexArray
• AddReplaceRule() : GromacsBlockModifier
• AddResidue() : Diag , ChainView , EntityView
• AddResidueRenamingRule() : Forcefield
• AddRevision() : MMCifInfoRevisions , MMCifInfo , MMCifInfoRevisions , MMCifInfo
• AddRow() : Table
• AddSecondaryConnector() : AtomImpl
• AddSequence() : SequenceViewObject , AlignmentHandle , SequenceListImpl , ConstSequenceList , SequenceList
• AddSink() : MultiLogSink
• AddSphere() : PrimList , IndexedVertexArray
• addState() : StateMachine
• AddStop() : GradientEdit
• AddString() : Diag
• AddSymmetricCompound() : SymmetrySettings
• AddText() : PrimList
• AddToken() : PythonContext
• AddTool() : ToolManager
• AddTorsion() : EditorBase , EntityImpl , ResidueImpl
• AddTrajectory() : TrajWidget
• addTransition() : State
• AddTri() : IndexedVertexArray , SurfaceImpl , SurfaceHandle
• AddTriN() : IndexedVertexArray
• AddUreyBradleyAngle() : Topology
• AddVertex() : SurfaceImpl , SurfaceHandle
• AddView() : EntityRenderer , SceneWin
• AddViewMode() : PanelBar
• AddWidget() : MainArea , PanelBar , PanelManager , ComboOptionsWidget , ToolBarOptionsWidget
• AddWidgetByName() : PanelManager
• AddWidgetToApp() : GostyApp
• AddWidgetToPool() : PanelManager
• AdjacencyBitmap() : AdjacencyBitmap
• AdjustPhaseOrigin() : ImageStateImpl< T, D >
• AdminRights() : AdminRights
• AdvanceProgress() : Progress
• AlgorithmBase() : AlgorithmBase
• Align() : AlignmentContextMenu , ChainMapper , _Aligner
• AlignedColumn() : AlignedColumn
• AlignedColumnIterator() : AlignedColumnIterator
• AlignedCuboid() : AlignedCuboid
• AlignedRegion() : AlignedRegion
• AlignmentChanged() : SequenceTableView , SequenceViewer
• AlignmentHandle() : AlignmentHandle
• AlignmentOpts() : AlignmentOpts
• alignments() : QSscorer
• AlignmentViewObject() : AlignmentViewObject
• AlignPropertiesPainter() : AlignPropertiesPainter
• AllCleared() : MessageWidget
• aln() : Scorer
• alns() : MappingResult , ContactScorer , QSScorer
• Alpha() : Color
• AminoAcidSet() : AminoAcidSet
• AminoAcidSetIterator() : AminoAcidSetIterator
• AnisotropicFilter() : AnisotropicFilter
• Append() : SequenceImpl , SequenceHandle
• AppendCode() : TextLogger
• AppendColorOp() : GfxObj
• AppendCommand() : ShellHistory
• AppendCommandlineArgument() : PythonInterpreter
• AppendError() : PythonShellWidget
• AppendModulePath() : PythonInterpreter
• AppendOutput() : PythonShellWidget , TextLogger
• AppendResidue() : EditorBase , ChainImpl
• Apply() : Entity , EntityRenderer , ConnectRendererBase , Transform , Rotation3 , Transform , Entity , BondHandle , Entity , GfxNode , GfxObj , ConnectRendererBase , EntityRenderer , TraceRendererBase , Scene , Selection , Surface , Transformation , ChainHandle , EntityImpl , CircleMask , CompositeMask , ConstData , TorsionHandle , ExtentMask , ImageHandle , ResidueView , ImageHandle , ConstImageHandle , TorsionImpl , ConstImageHandle , ChainView , ImageList , ChainImpl , ImageStateBase , ConnectorImpl , EntityView , ImageStateBase , ImageStateImpl< T, D > , ConstImageHandle , InfoHandle , InvertedMask , MaskBase , ResidueHandle , NullData , SphericalMask , InfoGroup , EntityView , InfoGroup , AtomView , InfoHandle , AtomView , AtomHandle , BondHandle , ImageStateImpl< T, D > , ChainView , EntityHandle , AtomImpl , PolygonMask , ResidueImpl , ResidueView , ImageStateBase , ImageStateImpl< T, D > , ImageList , ImageStateBase , ImageList , ImageHandle , ConstImageHandle , Transformation , ImageHandle , Data , Scene , Surface , EntityRenderer
• ApplyAxisRotation() : Transform
• ApplyInverse() : Transform
• ApplyIP() : ImageList , ImageHandle , ImageStateBase , ImageStateImpl< T, D > , ImageHandle , ImageList , ImageHandle , NullData , ImageStateImpl< T, D > , Data , ConstData , ImageHandle , ConstImageHandle , ImageList , ImageStateBase , ImageList , ImageHandle
• ApplyLBFGS() : Simulation
• ApplyOn() : Preset , RenderOp , VisibilityOp
• ApplyOnBuildingBlock() : HeuristicHydrogenConstructor , HeuristicBlockModifier , HydrogenConstructor , GromacsBlockModifier , BlockModifier , TerminiConstructor , GromacsHydrogenConstructor
• ApplyOnResidue() : GromacsHydrogenConstructor , HeuristicBlockModifier , BlockModifier , HeuristicHydrogenConstructor , HydrogenConstructor , TerminiConstructor , GromacsBlockModifier
• ApplyOptions() : Entity , RenderModeWidget
• ApplyRenderOptions() : CustomRenderOptions , CartoonRenderOptions , RenderOptions , CPKRenderOptions , LineRenderOptions , SlineRenderOptions , TraceRenderOptions
• ApplySD() : Simulation
• ApplyShiftToMask() : MaskOverlay
• ApplyTo() : EntityViewColorOp , BasicGradientColorOp , MapHandleColorOp , ByElementColorOp , MapHandleColorOp , UniformColorOp , ByChainColorOp , ColorOp , GradientLevelColorOp
• ApplyTransform() : CoordGroupHandle , XCSEditor , Vec3List , XCSEditor , CoordSource , EntityImpl
• ApplyXAxisRotation() : Transform
• ApplyXAxisTranslation() : Transform
• ApplyYAxisRotation() : Transform
• ApplyYAxisTranslation() : Transform
• ApplyZAxisRotation() : Transform
• ApplyZAxisTranslation() : Transform
• AreResiduesConsecutive() : Processor
• Argand() : Argand
• As() : ImageFormatBase
• AsBool() : InfoItem
• AsFloat() : InfoItem
• AsImage() : SimilarityMatrix
• AsInt() : InfoItem
• Assign() : GenericPropContainerImpl
• AssignFFSpecificNames() : Forcefield
• AssignGromacsNaming() : Modeller
• AssignPDBNaming() : Modeller
• AssignPreset() : SubstWeightMatrix
• AssignSecondaryStructure() : SecStructContextMenu , ChainHandle , ChainImpl
• AssignSecStructure() : MMCifReader
• AssignSSToA3M() : HHblits
• AsString() : ResNum
• AsVector() : InfoItem
• At() : Mat3 , Plane , Vec2 , Point , Ellipse2
• at() : ProfileHandle
• At() : Mat2
• at() : ProfileHandle
• At() : Mat4 , Mat3 , Line3 , Vec3 , Line2 , Mat2 , Point , Vec4 , Hyperbola2 , Vec3 , Vec2 , Mat4
• at() : ContextProfileDB
• AtAngle() : Ellipse2
• AtEnd() : RowSet< R > , LineIterator , IndexIterator , ShellHistory , ExtentIterator , IndexIterator< D >
• Atom() : Builder
• AtomBase() : AtomBase
• AtomEntry() : AtomEntry
• AtomGroupEntry() : AtomGroupEntry
• AtomHandle() : AtomHandle
• AtomImpl() : AtomImpl
• AtomProp() : AtomProp
• AtomSpec() : AtomSpec
• AtomView() : AtomView
• AtStart() : IndexIterator , ExtentIterator
• Attach() : SurfaceImpl , NullData , SurfaceImpl , Observable , ImageHandle , ConstData , SurfaceHandle , OverlayManager , ConstImageHandle
• AttachGfxObject() : SequenceViewObject
• AttachObserver() : SceneObserverImpl , EntityImpl , Scene , EntityHandle
• AttachRenderModeObserver() : SceneWinModel
• AttachView() : SequenceImpl , AlignmentHandle , SequenceHandle , SequenceImpl
• AutoAutoslab() : Scene
• AutoCorrelateFnc() : AutoCorrelateFnc
• AutomaticTransition() : AutomaticTransition
• Autoslab() : Scene
• AutoslabMax() : Scene