- a -

• A3MToCS() : HHblits
• A3MToProfile() : HHblits
• About() : InitMenuBar
• accept() : FileTypeDialog
• Acquire() : AdminRights
• Activate() : Tool
• ActivateOverlay() : OverlayManager
• ActivateTool() : ToolBar
• ActiveNodesChanged() : SceneWin , InspectorWidget
• ActiveToolChanged() : GLWin , ToolManager
• Add() : GfxNode , GradientPresetWidget , PresetEditor , GfxNode , PresetWidget , FastSphereRenderer , Scene , IndexedVertexArray , PointlistOverlay , ToolOptionEnum , WidgetPool , InfoSet , StarLoopDesc , PDBize , AminoAcidSet , SpatialOrganizer< ITEM, VEC > , GradientEdit
• add_scalar() : ImageStateImpl< T, D >
• AddAction() : ContextMenu , ToolBar
• AddAddRule() : GromacsBlockModifier
• AddAlignedSeq() : MMCifInfoStructRef
• AddAlignment() : SequenceViewer
• AddAllInclusiveBonds() : EntityView
• AddAltAtomPos() : EditorBase , ResidueImpl
• AddAngle() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddAtom() : 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
• AddChild() : SceneNode
• AddCitation() : MMCifInfo
• AddCMap() : BuildingBlock , Forcefield , GromacsBlockModifier , Topology
• AddCol() : Table
• AddCommand() : PythonInterpreterWorker
• AddCompound() : CompoundLib
• AddConstraint() : BuildingBlock , Forcefield
• AddContext() : PythonContext
• AddCyl() : PrimList
• AddCylinder() : IndexedVertexArray
• AddDefault() : InfoHandle
• AddDeleteAtom() : GromacsBlockModifier
• AddDiag() : Diagnostics
• AddDif() : MMCifInfoStructRefSeq
• AddDihedral() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddDisplayMode() : BaseViewObject
• AddDistanceConstraint() : Topology
• AddDockWidget() : MainWindow
• AddEntity() : SequenceViewer
• 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
• 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
• 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
• AddPresetToInfo() : PresetListModel
• AddProfile() : 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
• 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
• AlignedColumn() : AlignedColumn
• AlignedColumnIterator() : AlignedColumnIterator
• AlignedCuboid() : AlignedCuboid
• AlignedRegion() : AlignedRegion
• AlignmentChanged() : SequenceTableView , SequenceViewer
• AlignmentHandle() : AlignmentHandle
• AlignmentOpts() : AlignmentOpts
• AlignmentViewObject() : AlignmentViewObject
• AlignPropertiesPainter() : AlignPropertiesPainter
• AllCleared() : MessageWidget
• 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() : ConnectRendererBase , Entity , Transform , Rotation3 , Transform , Entity , GfxNode , GfxObj , ConnectRendererBase , EntityRenderer , TraceRendererBase , Scene , Selection , Surface , AtomHandle , Transformation , CircleMask , CompositeMask , ConstData , Data , ExtentMask , ImageHandle , ConstImageHandle , ResidueView , ConstImageHandle , ImageList , ImageStateBase , ResidueView , ImageStateBase , TorsionHandle , ImageStateImpl< T, D > , EntityView , ImageStateImpl< T, D > , InvertedMask , MaskBase , TorsionImpl , NullData , SphericalMask , AtomImpl , EntityImpl , InfoGroup , InfoHandle , ChainImpl , AtomView , BondHandle , AtomView , ChainHandle , ChainView , EntityHandle , EntityView , ConnectorImpl , ResidueImpl , BondHandle , ResidueHandle , ImageHandle , PolygonMask , InfoHandle , InfoGroup , ImageStateImpl< T, D > , ImageStateBase , ImageList , ConstImageHandle , ConnectRendererBase , ImageHandle , Surface , TraceRendererBase , EntityRenderer
• ApplyAxisRotation() : Transform
• ApplyInverse() : Transform
• ApplyIP() : ImageList , ImageStateImpl< T, D > , NullData , ImageList , ImageHandle , ImageStateBase , ImageHandle , Data , ImageHandle , ConstImageHandle , ImageList , ImageStateBase , ImageStateImpl< T, D > , ConstData , ImageHandle , ImageList , ImageStateImpl< T, D > , ImageList
• ApplyLBFGS() : Simulation
• ApplyOn() : VisibilityOp , RenderOp , Preset
• ApplyOnBuildingBlock() : GromacsBlockModifier , HydrogenConstructor , BlockModifier , GromacsHydrogenConstructor , HeuristicBlockModifier , TerminiConstructor , HeuristicHydrogenConstructor
• ApplyOnResidue() : GromacsHydrogenConstructor , HeuristicHydrogenConstructor , TerminiConstructor , GromacsBlockModifier , HydrogenConstructor , BlockModifier , HeuristicBlockModifier
• ApplyOptions() : Entity , RenderModeWidget
• ApplyRenderOptions() : TraceRenderOptions , CPKRenderOptions , SlineRenderOptions , CartoonRenderOptions , CustomRenderOptions , LineRenderOptions , RenderOptions
• ApplySD() : Simulation
• ApplyShiftToMask() : MaskOverlay
• ApplyTo() : UniformColorOp , MapHandleColorOp , BasicGradientColorOp , EntityViewColorOp , MapHandleColorOp , GradientLevelColorOp , ByChainColorOp , ByElementColorOp , ColorOp
• ApplyTransform() : EntityImpl , XCSEditor , CoordSource , CoordGroupHandle
• 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() : ChainHandle , ChainImpl
• AssignSecStructure() : MMCifReader
• AsString() : ResNum
• AsVector() : InfoItem
• At() : Line3 , Vec3 , Mat2 , Vec3 , Mat2 , Mat4 , Vec2 , Mat3 , Point , Line2 , Hyperbola2
• at() : ProfileHandle
• At() : Vec4 , Plane , Vec4 , Ellipse2 , Mat3 , Point
• AtAngle() : Ellipse2
• AtEnd() : IndexIterator< D > , LineIterator , RowSet< R > , ShellHistory , IndexIterator , ExtentIterator
• Atom() : Builder
• AtomBase() : AtomBase
• AtomEntry() : AtomEntry
• AtomGroupEntry() : AtomGroupEntry
• AtomHandle() : AtomHandle
• AtomImpl() : AtomImpl
• AtomProp() : AtomProp
• AtomSpec() : AtomSpec
• AtomView() : AtomView
• AtStart() : IndexIterator , ExtentIterator
• Attach() : NullData , ImageHandle , SurfaceImpl , OverlayManager , Observable , SurfaceHandle , ConstImageHandle , ConstData , SurfaceHandle , SurfaceImpl
• AttachGfxObject() : SequenceViewObject
• AttachObserver() : EntityHandle , SceneObserverImpl , Scene , EntityImpl
• AttachRenderModeObserver() : SceneWinModel
• AttachView() : AlignmentHandle , SequenceImpl , SequenceHandle
• AutoAutoslab() : Scene
• AutoCorrelateFnc() : AutoCorrelateFnc
• AutomaticTransition() : AutomaticTransition
• Autoslab() : Scene
• AutoslabMax() : Scene