Class Hierarchy

• Scientific.IO.PDB.Atom: Atom in a PDB structure
  • Scientific.IO.PDB.HetAtom: HetAtom in a PDB structure
• Scientific.Signals.Models.AutoRegressiveModel: Auto-regressive model for stochastic process
  • Scientific.Signals.Models.AveragedAutoRegressiveModel: Averaged auto-regressive model for stochastic process
• Scientific.Visualization.VRML2.Camera: Camera/viewpoint for a scene
• Scientific.IO.PDB.Chain: Chain of PDB residues
  • Scientific.IO.PDB.NucleotideChain: Nucleotide chain in a PDB file
  • Scientific.IO.PDB.PeptideChain: Peptide chain in a PDB file
• Scientific.Visualization.Color.Color: RGB Color specification
• Scientific.Visualization.Color.ColorScale: Mapping from a number interval to a color range
• Scientific.Functions.Derivatives.DerivVar: Numerical variable with automatic derivatives of arbitrary order
• Scientific.Functions.FirstDerivatives.DerivVar: Numerical variable with automatic derivatives of first order
• Scientific.IO.FortranFormat.FortranFormat: Parsed Fortran-style format string
• Scientific.IO.FortranFormat.FortranLine: Fortran-style record in formatted files
• Scientific.Geometry.Objects3D.GeometricalObject3D: Geometrical object in 3D space
  • Scientific.Geometry.Objects3D.Circle: Circle
  • Scientific.Geometry.Objects3D.Cone: Cone
  • Scientific.Geometry.Objects3D.Line: Line
  • Scientific.Geometry.Objects3D.Plane: Plane
  • Scientific.Geometry.Objects3D.Sphere: Sphere
• Scientific.Visualization.VPython.GraphicsObject: Graphics object for VPython
  • Scientific.Visualization.VPython.Material: Material specification for graphics objects
  • Scientific.Visualization.VPython.ShapeObject: Graphics objects representing geometrical shapes
    • Scientific.Visualization.VPython.Arrow: Arrow
    • Scientific.Visualization.VPython.Cone: Cone
    • Scientific.Visualization.VPython.Cube: Cube
    • Scientific.Visualization.VPython.Cylinder: Cylinder
    • Scientific.Visualization.VPython.PolyLines: Multiple connected lines
      • Scientific.Visualization.VPython.Line: Line
    • Scientific.Visualization.VPython.Polygons: Polygons
    • Scientific.Visualization.VPython.Sphere: Sphere
• Tkinter.Grid: Geometry manager Grid.
  • Tkinter.Widget: Internal class.
    • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
      • Scientific.TkWidgets.ButtonBar: Horizontal array of buttons
      • Scientific.TkWidgets.FilenameEntry: Filename entry widget
      • Scientific.TkWidgets.FloatEntry: Entry field for float numbers
        • Scientific.TkWidgets.IntEntry: Entry field for integer numbers
      • Scientific.TkWidgets.TkPlotCanvas.PlotCanvas: Tk plot widget
      • Scientific.TkWidgets.StatusBar: Status bar
      • Scientific.TkWidgets.TkVisualizationCanvas.VisualizationCanvas: Tk visualization widget
• Scientific.Visualization.VRML.Group: Base class for composite objects
  • Scientific.Visualization.VRML.Arrow: Arrow
• Scientific.Visualization.VRML2.Group: Base class for composite objects
  • Scientific.Visualization.VRML2.Arrow: Arrow
• Scientific.IO.PDB.Group: Atom group (residue or molecule) in a PDB file
  • Scientific.IO.PDB.Molecule: Molecule in a PDB file
  • Scientific.IO.PDB.Residue
    • Scientific.IO.PDB.AminoAcidResidue: Amino acid residue in a PDB file
    • Scientific.IO.PDB.NucleotideResidue: Nucleotide residue in a PDB file
• Scientific.Visualization.VMD.Group: Base class for composite objects
  • Scientific.Visualization.VMD.Arrow: Arrow
• Scientific.Visualization.PyMOL.Group: Base class for composite objects
  • Scientific.Visualization.PyMOL.Arrow: Arrow
• Scientific.Visualization.VPython.Group: Base class for composite objects
• Scientific.Statistics.Histogram.Histogram: Histogram in one variable
  • Scientific.Statistics.Histogram.WeightedHistogram: Weighted histogram in one variable
• code.InteractiveInterpreter: Base class for InteractiveConsole.
  • code.InteractiveConsole: Closely emulate the behavior of the interactive Python interpreter.
    • Scientific.BSP.Console.ParallelConsole
  • Scientific.BSP.Console.ParallelInterpreter
• Scientific.Functions.Interpolation.InterpolatingFunction: Function defined by values on a grid using interpolation
  • Scientific.Functions.Interpolation.NetCDFInterpolatingFunction: Function defined by values on a grid in a netCDF file
  • Scientific.Geometry.TensorAnalysis.TensorField: Tensor field of arbitrary rank
    • Scientific.Geometry.TensorAnalysis.ScalarField: Scalar field (tensor field of rank 0)
    • Scientific.Geometry.TensorAnalysis.VectorField: Vector field (tensor field of rank 1)
• Scientific.Geometry.Objects3D.Lattice
  • Scientific.Geometry.Objects3D.RhombicLattice: Lattice with rhombic elementary cell
    • Scientific.Geometry.Objects3D.BravaisLattice: General Bravais lattice
      • Scientific.Geometry.Objects3D.SCLattice: Simple cubic lattice
• Scientific.MPI.IO.LogFile: File for logging events from all processes
• Scientific.MPI.MPICommunicator: MPI Communicator
• Scientific.MPI.MPIOperationObject
  • Scientific.MPI.band: The 'bitwise and' operation in reduce/allreduce communications.
  • Scientific.MPI.bor: The 'bitwise or' operation in reduce/allreduce communications.
  • Scientific.MPI.bxor: The 'bitwise exclusive-or' operation.
  • Scientific.MPI.land: The 'logical and' operation in reduce/allreduce communications.
  • Scientific.MPI.lor: The 'logical or' operation in reduce/allreduce communications.
  • Scientific.MPI.lxor: The 'logical exclusive-or' operation.
  • Scientific.MPI.max: The 'maximum' operation in reduce/allreduce communications.
  • Scientific.MPI.maxloc: The 'location of the maximum' operation.
  • Scientific.MPI.min: The 'minimum' operation in reduce/allreduce communications.
  • Scientific.MPI.minloc: The 'location of the minimum' operation.
  • Scientific.MPI.prod: The 'product' operation in reduce/allreduce communications.
  • Scientific.MPI.replace: The 'replace' operation.
  • Scientific.MPI.sum: The 'sum' operation in reduce/allreduce communications.
• Scientific.MPI.MPIRequest: MPI Request
• Tkinter.Misc: Internal class.
  • Tkinter.BaseWidget: Internal class.
    • Tkinter.Toplevel: Toplevel widget, e.g.
      • Scientific.TkWidgets.ModalDialog
    • Tkinter.Widget: Internal class.
      • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
        • Scientific.TkWidgets.ButtonBar: Horizontal array of buttons
        • Scientific.TkWidgets.FilenameEntry: Filename entry widget
        • Scientific.TkWidgets.FloatEntry: Entry field for float numbers
          • Scientific.TkWidgets.IntEntry: Entry field for integer numbers
        • Scientific.TkWidgets.TkPlotCanvas.PlotCanvas: Tk plot widget
        • Scientific.TkWidgets.StatusBar: Status bar
        • Scientific.TkWidgets.TkVisualizationCanvas.VisualizationCanvas: Tk visualization widget
• Scientific.Visualization.VRML2.NavigationInfo: Navigation information
• Scientific.IO.NetCDF.NetCDFFile: netCDF file
• Scientific.IO.NetCDF.NetCDFVariable: Variable in a netCDF file
• Scientific.BSP.Console.OKToken
• Pyro.core.ObjBase
  • Scientific.DistributedComputing.TaskManager.TaskManager: Manager for computational tasks.
• Scientific.BSP.Console.OutputStream
• Scientific.IO.PDB.PDBFile: PDB file with access at the record level
• Tkinter.Pack: Geometry manager Pack.
  • Tkinter.Widget: Internal class.
    • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
      • Scientific.TkWidgets.ButtonBar: Horizontal array of buttons
      • Scientific.TkWidgets.FilenameEntry: Filename entry widget
      • Scientific.TkWidgets.FloatEntry: Entry field for float numbers
        • Scientific.TkWidgets.IntEntry: Entry field for integer numbers
      • Scientific.TkWidgets.TkPlotCanvas.PlotCanvas: Tk plot widget
      • Scientific.TkWidgets.StatusBar: Status bar
      • Scientific.TkWidgets.TkVisualizationCanvas.VisualizationCanvas: Tk visualization widget
• Scientific.Physics.PhysicalQuantities.PhysicalQuantity: Physical quantity with units
• Scientific.Physics.PhysicalQuantities.PhysicalUnit: Physical unit
• Tkinter.Place: Geometry manager Place.
  • Tkinter.Widget: Internal class.
    • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
      • Scientific.TkWidgets.ButtonBar: Horizontal array of buttons
      • Scientific.TkWidgets.FilenameEntry: Filename entry widget
      • Scientific.TkWidgets.FloatEntry: Entry field for float numbers
        • Scientific.TkWidgets.IntEntry: Entry field for integer numbers
      • Scientific.TkWidgets.TkPlotCanvas.PlotCanvas: Tk plot widget
      • Scientific.TkWidgets.StatusBar: Status bar
      • Scientific.TkWidgets.TkVisualizationCanvas.VisualizationCanvas: Tk visualization widget
• Scientific.QtWidgets.QtPlotCanvas.PlotGraphics: Compound graphics object
• Scientific.TkWidgets.TkPlotCanvas.PlotGraphics: Compound graphics object
• Scientific.QtWidgets.QtPlotCanvas.PolyPoints
  • Scientific.QtWidgets.QtPlotCanvas.PolyLine: Multiple connected lines
    • Scientific.QtWidgets.QtPlotCanvas.HorizontalLine: A horizontal line
    • Scientific.QtWidgets.QtPlotCanvas.VerticalLine: A vertical line
  • Scientific.QtWidgets.QtPlotCanvas.PolyMarker: Series of markers
• Scientific.TkWidgets.TkPlotCanvas.PolyPoints
  • Scientific.TkWidgets.TkPlotCanvas.PolyLine: Multiple connected lines
    • Scientific.TkWidgets.TkPlotCanvas.HorizontalLine: A horizontal line
    • Scientific.TkWidgets.TkPlotCanvas.VerticalLine: A vertical line
  • Scientific.TkWidgets.TkPlotCanvas.PolyMarker: Series of markers
• Scientific.QtWidgets.QtVisualizationCanvas.PolyPoints3D
  • Scientific.QtWidgets.QtVisualizationCanvas.PolyLine3D: Multiple connected lines
• Scientific.TkWidgets.TkVisualizationCanvas.PolyPoints3D
  • Scientific.TkWidgets.TkVisualizationCanvas.PolyLine3D: Multiple connected lines
• Scientific.Functions.Polynomial.Polynomial: Multivariate polynomial
• Scientific.Physics.Potential.PotentialWithGradients
• Scientific.Physics.Potential.PotentialWithGradientsAndForceConstants
• Scientific.Visualization.PyMOL.PyMOLObject: Graphics object for PyMOL
  • Scientific.Visualization.PyMOL.Material: Material specification for graphics objects
  • Scientific.Visualization.PyMOL.Molecules: Molecules from a PDB file
  • Scientific.Visualization.PyMOL.ShapeObject: Graphics objects representing geometrical shapes
    • Scientific.Visualization.PyMOL.Cone: Cone
    • Scientific.Visualization.PyMOL.Cube: Cube
    • Scientific.Visualization.PyMOL.Cylinder: Cylinder
    • Scientific.Visualization.PyMOL.Line: Line
    • Scientific.Visualization.PyMOL.Sphere: Sphere
• Scientific.QtWidgets.qt_fake.QWidget
  • Scientific.QtWidgets.QtPlotCanvas.PlotCanvas: Qt plot widget
  • Scientific.QtWidgets.QtVisualizationCanvas.VisualizationCanvas: Qt visualization widget
• Scientific.Geometry.Quaternion.Quaternion: Quaternion (hypercomplex number)
• Scientific.Functions.Rational.RationalFunction: Rational Function
• Scientific.IO.PDB.ResidueNumber: PDB residue number
• Scientific.Visualization.VRML.Scene: VRML scene
• Scientific.Visualization.VRML2.Scene: VRML scene
• Scientific.Visualization.VMD.Scene: VMD scene
• Scientific.Visualization.VPython.Scene: VPython scene
• Scientific.Visualization.PyMOL.Scene: PyMOL scene
• Scientific.Visualization.VRML2.SceneFile
• Scientific.Visualization.VRML.SceneFile
• Scientific.Visualization.VMD.SceneFile
• Scientific.IO.PDB.Structure: A high-level representation of the contents of a PDB file
• Scientific.Visualization.Color.SymmetricColorScale: Mapping of a symmetric number interval to a color range
• Scientific.Threading.TaskManager.TaskManager: Parallel task manager for shared-memory multiprocessor machines
• Scientific.Geometry.Tensor: Tensor in 3D space
• Scientific.IO.TextFile.TextFile: Text files with line iteration and transparent compression
• Scientific.Geometry.Transformation.Transformation: Linear coordinate transformation.
  • Scientific.Geometry.Transformation.LinearTransformation: General linear transformation.
  • Scientific.Geometry.Transformation.RigidBodyTransformation: Combination of translations and rotations
    • Scientific.Geometry.Transformation.Rotation: Rotational transformation
    • Scientific.Geometry.Transformation.RotationTranslation: Combined translational and rotational transformation.
    • Scientific.Geometry.Transformation.Translation: Translational transformation
  • Scientific.Geometry.Transformation.Scaling: Scaling
    • Scientific.Geometry.Transformation.Inversion
  • Scientific.Geometry.Transformation.Shear
• UserDict.UserDict
  • Scientific.DictWithDefault.DictWithDefault: Dictionary with default values
• Scientific.Visualization.VMD.VMDObject: Graphics object for VMD
  • Scientific.Visualization.VMD.Material: Material specification for graphics objects
  • Scientific.Visualization.VMD.Molecules: Molecules from a PDB file
  • Scientific.Visualization.VMD.ShapeObject: Graphics objects representing geometrical shapes
    • Scientific.Visualization.VMD.Cone: Cone
    • Scientific.Visualization.VMD.Cube: Cube
    • Scientific.Visualization.VMD.Cylinder: Cylinder
    • Scientific.Visualization.VMD.Line: Line
    • Scientific.Visualization.VMD.Sphere: Sphere
• Scientific.Visualization.VRML.VRMLObject: Graphics object for VRML
  • Scientific.Visualization.VRML.Material: Material specification for graphics objects
  • Scientific.Visualization.VRML.ShapeObject: Graphics objects representing geometrical shapes
    • Scientific.Visualization.VRML.Cube: Cube
    • Scientific.Visualization.VRML.Line: Line
    • Scientific.Visualization.VRML.LinearOrientedObject
      • Scientific.Visualization.VRML.Cone: Cone
      • Scientific.Visualization.VRML.Cylinder: Cylinder
    • Scientific.Visualization.VRML.PolyLines: Multiple connected lines
    • Scientific.Visualization.VRML.Polygons: Polygons
    • Scientific.Visualization.VRML.Sphere: Sphere
• Scientific.Visualization.VRML2.VRMLObject: Graphics object for VRML
  • Scientific.Visualization.VRML2.Material: Material specification for graphics objects
  • Scientific.Visualization.VRML2.ShapeObject: Graphics objects representing geometrical shapes
    • Scientific.Visualization.VRML2.Cube: Cube
    • Scientific.Visualization.VRML2.Line: Line
    • Scientific.Visualization.VRML2.LinearOrientedObject
      • Scientific.Visualization.VRML2.Cone: Cone
      • Scientific.Visualization.VRML2.Cylinder: Cylinder
    • Scientific.Visualization.VRML2.PolyLines: Multiple connected lines
    • Scientific.Visualization.VRML2.Polygons: Polygons
    • Scientific.Visualization.VRML2.Sphere: Sphere
• Scientific.Geometry.Vector: Vector in 3D space
• Scientific.TkWidgets.TkVisualizationCanvas.VisualizationGraphics: Compound graphics object
• Scientific.QtWidgets.QtVisualizationCanvas.VisualizationGraphics: Compound graphics object
• Tkinter.Wm: Provides functions for the communication with the window manager.
  • Tkinter.Toplevel: Toplevel widget, e.g.
    • Scientific.TkWidgets.ModalDialog
• object: The most base type
  • exceptions.BaseException: Common base class for all exceptions
    • exceptions.Exception: Common base class for all non-exit exceptions.
      • Scientific.BSP.Console.BSPSyncError
      • exceptions.StandardError: Base class for all standard Python exceptions that do not represent interpreter exiting.
        • exceptions.ValueError: Inappropriate argument value (of correct type).
          • Scientific.IterationCountExceededError
      • Scientific.DistributedComputing.TaskManager.TaskManagerTermination: Signals that the task manager has no more tasks to handle.
      • Scientific.DistributedComputing.TaskManager.TaskRaisedException: Signals that an exception was raised inside a task.
  • Scientific.Clustering.AffinityPropagation.DataSet: A collection of data items with similarities
  • Scientific.DistributedComputing.MasterSlave.GlobalStateValue
  • Scientific.DistributedComputing.MasterSlave.MasterProcess: Master process in a master-slave setup
  • Scientific.BSP.ParBase: Distributed data base class
  • Scientific.BSP.ParClass: Global class
  • Scientific.BSP.ParIndex: Parallel index value
  • Scientific.BSP.ParIndexIterator: Parallel index iterator
  • Scientific.BSP.ParIterator: Parallel iterator
  • Scientific.BSP.ParValue: Global data
    • Scientific.BSP.ParAccumulator: Global accumulator
    • Scientific.BSP.ParConstant: Global constant
    • Scientific.BSP.ParData: Global data
    • Scientific.BSP.ParFunction: Global function
      • Scientific.BSP.ParRootFunction: Asymmetric global function
    • Scientific.BSP.ParMessages: Global message list
    • Scientific.BSP.ParSequence: Global distributed sequence
      • Scientific.BSP.ParRootSequence: Global distributed sequence with data taken from processor 0
    • Scientific.BSP.ParTuple: Global data tuple
  • Scientific.DistributedComputing.MasterSlave.SlaveProcess: Slave process in a master-slave setup
  • Scientific.IO.PDBSpaceGroups.SpaceGroup
  • Scientific.DistributedComputing.TaskManager.Task: Describes a task inside the task manager.
  • Scientific.DistributedComputing.TaskManager.TaskQueue: A FIFO queue for tasks.
  • Scientific.DistributedComputing.TaskManager.Watchdog: A background process that watches compute tasks and unregisters those that do not ping the task manager at the promised interval.
  • dict: dict() -> new empty dictionary.
    • Scientific.NumberDict.NumberDict: Dictionary storing numerical values
  • float: float(x) -> floating point number
  • int: int(x[, base]) -> integer