- a -

• A3MToCS() : HHblits
• A3MToProfile() : HHblits
• Add() : StarLoopDesc , Distances , Dist2Mean , StarLoopDesc , AminoAcidSet , PDBize , SpatialOrganizer< ITEM, VEC >
• add_scalar() : ImageStateImpl< T, D >
• AddAddRule() : GromacsBlockModifier
• AddAlignedSeq() : MMCifInfoStructRef
• AddAllInclusiveBonds() : EntityView
• AddAltAtomPos() : ResidueImpl , EditorBase
• AddAngle() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddAssembly() : LinearIndexer
• AddAtom() : Compound , Diag , ChainView , EntityView , BuildingBlock , ResidueView
• AddAtomInternal() : EntityView
• AddAtomRenamingRule() : Forcefield
• AddAuthorsToCitation() : MMCifInfo
• AddBioUnit() : MMCifInfo
• AddBlockModifier() : Forcefield
• AddBond() : Compound , AtomView , EntityView , BuildingBlock , Forcefield , GromacsBlockModifier
• AddBuildingBlock() : Forcefield
• AddCallback() : Progress
• AddChain() : Diag , MMCifInfoBioUnit , EntityView
• AddCharacters() : LinearCharacterContainer
• AddCitation() : MMCifInfo
• AddCMap() : BuildingBlock , Forcefield , GromacsBlockModifier , Topology
• AddCol() : Table
• AddColumn() : ProfileHandle
• AddCompound() : CompoundLib
• AddConstraint() : BuildingBlock , Forcefield
• AddDeleteAtom() : GromacsBlockModifier
• AddDiag() : Diagnostics
• AddDif() : MMCifInfoStructRefSeq
• AddDihedral() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddDistance() : DistanceMap
• AddDistanceConstraint() : Topology
• addError() : _XMLTestResult
• AddExclusion() : BuildingBlock , Topology
• addFailure() : _XMLTestResult
• AddFGMDHBondAcceptor() : Topology
• AddFGMDHBondDonor() : Topology
• AddFrame() : CoordGroupHandle , CoordSource , InMemCoordSource
• AddFrames() : CoordGroupHandle
• AddHarmonicAngle() : Topology
• AddHarmonicBond() : Topology
• AddHarmonicDistanceRestraint() : Topology
• AddHarmonicImproper() : Topology
• AddHarmonicPositionRestraint() : Topology
• AddHydrogenConstructor() : Forcefield
• AddHydrogenRule() : GromacsHydrogenConstructor
• AddImplicitGenborn() : Forcefield
• AddImproper() : BuildingBlock , Forcefield , GromacsBlockModifier
• AddInt() : Diag
• AddLJ() : Forcefield
• AddLJPair() : Forcefield , Topology
• AddMass() : Forcefield
• AddMMCifEntityIdTr() : MMCifInfo
• AddMMCifPDBChainTr() : MMCifInfo
• AddNode() : Polygon2 , PolygonMask
• AddOperation() : MMCifInfo
• AddOperations() : MMCifInfoBioUnit
• addParticle() : DensityForce
• AddPDBMMCifChainTr() : MMCifInfo
• AddPeriodicDihedral() : Topology
• AddPeriodicImproper() : Topology
• AddPoint() : PointCloud
• AddPointCloud() : PointCloudManager
• AddPositionConstraint() : Simulation , Topology
• AddPositionConstraints() : Simulation
• AddPositions() : LinearPositionContainer
• AddProfile() : ProfileDB
• AddReplaceRule() : GromacsBlockModifier
• AddResidue() : Diag , ChainView , EntityView
• AddResidueRenamingRule() : Forcefield
• AddRevision() : MMCifInfoRevisions , MMCifInfo , MMCifInfoRevisions , MMCifInfo
• AddRow() : Table
• AddSecondaryConnector() : AtomImpl
• AddSequence() : AlignmentHandle , SequenceListImpl , ConstSequenceList , SequenceList
• AddSink() : MultiLogSink
• AddString() : Diag
• AddTorsion() : EditorBase , EntityImpl , ResidueImpl
• AddTri() : SurfaceImpl , SurfaceHandle
• AddUreyBradleyAngle() : Topology
• AddVertex() : SurfaceImpl , SurfaceHandle
• AdjacencyBitmap() : AdjacencyBitmap
• AdjustPhaseOrigin() : ImageStateImpl< T, D >
• AdvanceProgress() : Progress
• AlgorithmBase() : AlgorithmBase
• AlignedColumn() : AlignedColumn
• AlignedColumnIterator() : AlignedColumnIterator
• AlignedCuboid() : AlignedCuboid
• AlignedRegion() : AlignedRegion
• AlignmentHandle() : AlignmentHandle
• AlignmentOpts() : AlignmentOpts
• alignments() : QSscorer
• AminoAcidSet() : AminoAcidSet
• AminoAcidSetIterator() : AminoAcidSetIterator
• AnisotropicFilter() : AnisotropicFilter
• Append() : SequenceImpl , SequenceHandle
• AppendResidue() : EditorBase , ChainImpl
• Apply() : ResidueHandle , EntityView , ImageHandle , ConnectorImpl , AtomView , ImageStateImpl< T, D > , ConstData , NullData , ImageStateBase , ConstImageHandle , Transformation , ImageList , Rotation3 , Transform , Transformation , CircleMask , CompositeMask , Data , ExtentMask , ImageHandle , ConstImageHandle , ImageList , ImageStateBase , ImageStateImpl< T, D > , InvertedMask , MaskBase , PolygonMask , SphericalMask , AtomHandle , AtomView , BondHandle , ChainHandle , ChainView , EntityHandle , EntityView , AtomImpl , ChainImpl , EntityImpl , ResidueImpl , TorsionImpl , ResidueView , TorsionHandle
• ApplyAxisRotation() : Transform
• ApplyInverse() : Transform
• ApplyIP() : ImageHandle , ImageList , ImageStateBase , ImageStateImpl< T, D > , ConstData , ImageStateImpl< T, D > , NullData , ImageStateImpl< T, D > , ImageStateBase , ImageList , ImageHandle , ConstImageHandle , Data , ImageHandle
• ApplyLBFGS() : Simulation
• ApplyOnBuildingBlock() : TerminiConstructor , HeuristicHydrogenConstructor , HeuristicBlockModifier , BlockModifier , GromacsHydrogenConstructor , GromacsBlockModifier , HydrogenConstructor
• ApplyOnResidue() : HydrogenConstructor , BlockModifier , HeuristicBlockModifier , GromacsHydrogenConstructor , GromacsBlockModifier , HeuristicHydrogenConstructor , TerminiConstructor
• ApplySD() : Simulation
• ApplyTransform() : CoordGroupHandle , EntityImpl , XCSEditor , CoordSource , XCSEditor
• ApplyXAxisRotation() : Transform
• ApplyXAxisTranslation() : Transform
• ApplyYAxisRotation() : Transform
• ApplyYAxisTranslation() : Transform
• ApplyZAxisRotation() : Transform
• ApplyZAxisTranslation() : Transform
• AreResiduesConsecutive() : Processor
• As() : ImageFormatBase
• AsImage() : SimilarityMatrix
• Assign() : GenericPropContainerImpl
• AssignFFSpecificNames() : Forcefield
• AssignGromacsNaming() : Modeller
• AssignPDBNaming() : Modeller
• AssignPreset() : SubstWeightMatrix
• AssignSecondaryStructure() : ChainHandle , ChainImpl
• AssignSecStructure() : MMCifReader
• AsString() : ResNum
• At() : Hyperbola2 , Line2 , Ellipse2 , Vec2 , Mat2 , Mat4 , Vec3 , Vec4 , Vec2
• at() : ProfileHandle
• At() : Vec4 , Vec3 , Point , Mat4 , Mat3 , Plane , Line3 , Mat3 , Mat2
• AtAngle() : Ellipse2
• AtEnd() : LineIterator , IndexIterator , RowSet< R > , ExtentIterator , IndexIterator< D >
• Atom() : Builder
• AtomBase() : AtomBase
• AtomGroupEntry() : AtomGroupEntry
• AtomHandle() : AtomHandle
• AtomImpl() : AtomImpl
• AtomProp() : AtomProp
• AtomSpec() : AtomSpec
• AtomView() : AtomView
• AtStart() : ExtentIterator , IndexIterator
• Attach() : SurfaceHandle , ConstImageHandle , SurfaceImpl , NullData , ConstData , Observable , SurfaceHandle , SurfaceImpl , ImageHandle
• AttachObserver() : EntityImpl , EntityHandle
• AttachView() : SequenceImpl , AlignmentHandle , SequenceHandle , SequenceImpl , SequenceHandle
• AutoCorrelateFnc() : AutoCorrelateFnc