Class Hierarchy

• schrodinger.application.desmond.enhsamp.ASLObject
• urllib2.AbstractBasicAuthHandler
  • urllib2.ProxyBasicAuthHandler
    • schrodinger.utils.urllib.ProxyBasicAuthHandler
• urllib2.AbstractDigestAuthHandler
  • urllib2.ProxyDigestAuthHandler
    • schrodinger.utils.urllib.ProxyDigestAuthHandler
• schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer: Convert a structure file of screen results (or inputs) into active and decoy fingerprints and report similarity metrics between the fingerprint sets.
• schrodinger.protein.findhets.AddNeighborGroups: For each untemplated atom that is bound to a templated het, create a list of atoms that it is bound to that are not templated.
• schrodinger.job.app.App: A class to handle all aspects of job setup and running.
• schrodinger.structutils.assignbondorders.AssignBondOrders
• schrodinger.application.desmond.gui.AtomGroupRow
• schrodinger.pipeline.pipeutils.BackwardsReader: Read a file line by line, backwards.
• urllib2.BaseHandler
  • urllib2.AbstractHTTPHandler
    • urllib2.HTTPHandler
      • schrodinger.utils.urllib.MyHTTPHandler
    • urllib2.HTTPSHandler
      • schrodinger.utils.urllib.HTTPSHandler
        • schrodinger.utils.urllib.MyHTTPSHandler
  • urllib2.ProxyBasicAuthHandler
    • schrodinger.utils.urllib.ProxyBasicAuthHandler
  • urllib2.ProxyDigestAuthHandler
    • schrodinger.utils.urllib.ProxyDigestAuthHandler
  • urllib2.ProxyHandler
    • schrodinger.utils.urllib.ProxyHandler: A ProxyHandler subclass that loads its proxy configuration from 'web_proxy.json' file in the Schrodinger app data directory.
• schrodinger.structutils.sitealign.BindingSiteAligner: Align structures by matching binding site atoms.
• schrodinger.application.desmond.meta.CV: base class for collective variable
  • schrodinger.application.desmond.meta.CVAngle: A class to define angle collective variable.
  • schrodinger.application.desmond.meta.CVDihedral: A class to define dihedral collective variable.
  • schrodinger.application.desmond.meta.CVDist: distance collective variable
  • schrodinger.application.desmond.meta.CVrmsd: rmsd collective variable
  • schrodinger.application.desmond.meta.CVzdist0: This collective variable reports an absolute Z-distance from the origin (z=0).
• schrodinger.protein.captermini.CapTermini
• schrodinger.ui.widgettable.CellIterator: column.cell row.cell Class for iterating over cells in a row or column and for getting a cell Cells are indexed starting with 1 Ex: cell = row.cell[1] or: cell = column.cell[1]
• schrodinger.application.macromodel.utils.CluUtil: A class for writing and running Cluster clu files.
• schrodinger.application.desmond.meta.CmsModel
• schrodinger.structutils.color.ColorScheme: Define a Maestro color scheme.
• schrodinger.ui.widgettable.ColumnIterator: table.column Class for iterating over columns and getting a column Ex: column = table.column[colid]
• schrodinger.application.macromodel.utils.ComUtil: A class for writing MacroModel com files.
  • schrodinger.application.macromodel.utils.ComUtilAppSci: Subclass of ComUtil with defaults that are closer to the current Maestro version.
    • schrodinger.application.macromodel.utils.ComUtil_2010: This class will be deprecated in the next release.
• schrodinger.application.glide.poseviewconvert.Complex: A helper class to split a receptor-ligand complex structure into ligand, and receptor structure components, and write the structure components to new files.
• schrodinger.structutils.rmsd.ConformerRmsd: A class to calculate the root mean square deviatation between the atomic coordinates of two conformer structure.Structure objects.
• schrodinger.structutils.rmsd.ConformerRmsdX: A class to calculate the root mean square deviatation between the atomic coordinates of two conformer structure.Structure objects.
• schrodinger.application.bioluminate.protein.Consensus: Access the atoms, residues, and molecules (or just their indices) that are considered to be consensus objects for a template structure and query structure.
• schrodinger.application.glide.glide.Constraint: Class defining a docking constraint in the receptor.
  • schrodinger.application.glide.glide.AcceptorConstraint: H-Bond constraint that was specified as a *receptor* acceptor atom.
  • schrodinger.application.glide.glide.DonorConstraint: H-Bond constraint that was specified as a *receptor* donor atom.
  • schrodinger.application.glide.glide.HydrophobicConstraint
  • schrodinger.application.glide.glide.MetalConstraint: This constraint was specified as a metal receptor atom.
  • schrodinger.application.glide.glide.NOEConstraint
  • schrodinger.application.glide.glide.PositionalConstraint
• schrodinger.application.glide.glide.ConstraintGroup: Class defining a constraint group.
• schrodinger.utils.ligfilter.Criterion: A base class for a structure matching criterion.
  • schrodinger.utils.ligfilter.AslCriterion: This criterion considers a Structure as matching if the stored ASL expresson match returns at least one atom.
  • schrodinger.utils.ligfilter.PredefinedCriterion: A structure matching criterion that acts on the value of a predefined function applied to the structure.
  • schrodinger.utils.ligfilter.PropertyCriterion: A structure matching criterion that acts on the presence or value of a specific structure property.
  • schrodinger.utils.ligfilter.SmartsCriterion: A structure matching criterion that looks for a match to a Definition instance, which is comprised of a collection of SMARTS patterns.
• schrodinger.utils.ligfilter.CriterionParser: A class for parsing a general property or predefined matching criterion.
• schrodinger.application.mcpro.modelsystemwizard.ModelSystem.CtObj: This class is created to group together all relevant data about a structure and to provide functions for displaying the structure on Maestro workspace easily.
• schrodinger.utils.ligfilter.Definition: A class that defines a collection of SMARTS patterns for matching against.
• schrodinger.utils.ligfilter.DefinitionParser: A class for parsing a (possibly multi-line) specification of a Definition.
• schrodinger.application.desmond.system_builder_util.DesmondBoxSize
• schrodinger.trajectory.desmondsimulation.DesmondSimulation
  • schrodinger.trajectory.desmondsimulation.FepSimulation: A class for handling Fep Simulation
• schrodinger.ui.qt.appframework.DialogParameters: Class for holding dialog parameters.
• schrodinger.ui.appframework.DialogParameters: Class for holding dialog parameters.
• UserDict.DictMixin
  • schrodinger.infra.mmim.MMIMDict: A class for setting and getting MMIM keyword values.
  • schrodinger.application.desmond.ffiostructure._ElementProperty: A dictionary of other_block element based properties.
    • schrodinger.application.desmond.ffiostructure._FEPIOElementProperty: hash(x)
    • schrodinger.application.desmond.ffiostructure._FFIOElementProperty: hash(x)
  • schrodinger.application.desmond.ffiostructure._FEPIOProperty: A dictionary of fepio properties, with all dict methods.
  • schrodinger.application.desmond.ffiostructure._FEPIOSubBlockProperty: A dictionary of fepio sub-block properties.
  • schrodinger.trajectory.ffstructure._FFAngleProperty: A dictionary to hold angle force field parameters.
  • schrodinger.trajectory.ffstructure._FFBondProperty: A dictionary to hold bond force field parameters.
  • schrodinger.trajectory.ffstructure._FFConstraintProperty: A dictionary to hold constraint force field parameters.
  • schrodinger.trajectory.ffstructure._FFDihedralProperty: A dictionary to hold dihedral force field parameters.
  • schrodinger.trajectory.ffstructure._FFExclusionProperty: A dictionary to hold exclusion pair force field parameters.
  • schrodinger.application.desmond.ffiostructure._FFIOProperty: A dictionary of ffio properties, with all dict methods.
  • schrodinger.application.desmond.ffiostructure._FFIOSubBlockProperty: A dictionary of ffio sub-block properties.
  • schrodinger.trajectory.ffstructure._FFPairProperty: A dictionary to hold pair force field parameters.
  • schrodinger.trajectory.ffstructure._FFPseudoProperty: A dictionary to hold pseudo atom force field parameters.
  • schrodinger.trajectory.ffstructure._FFRestraintProperty: A dictionary to hold restraint force field parameters.
  • schrodinger.trajectory.ffstructure._FFSiteProperty: A dictionary to hold site force field parameters.
  • schrodinger.trajectory.ffstructure._FFVdwtypeProperty: A dictionary to hold Van der Waals type force field parameters.
  • schrodinger.trajectory.ffstructure._FFVirtualProperty: A dictionary to hold virtual site force field parameters.
  • schrodinger.application.qsite.input._GenDict: A dictionary-like class for getting and setting keywords in the &gen section of qsite input, which controls the Jaguar portion of the calculation.
  • schrodinger.application.qsite.input._MopacDict: A dictionary-like class for getting and setting keywords in the &mopac section of qsite input, which controls the Jaguar/MOPAC portion of the calculation.
  • schrodinger.structure._StructureAtomProperty: A dictionary of atom based properties.
  • schrodinger.structure._StructureBondProperty: A dictionary of bond based properties.
  • schrodinger.structure._StructureProperty: A dictionary of Structure based properties, with all dict methods.
• schrodinger.pipeline.pipeutils.DotPrinter: Class for printing a progress period or percentage every N number of iterations.
• schrodinger.pipeline.stage.DotPrinter: Class for printing a progress period or percentage every N number of iterations.
• schrodinger.application.mcpro.ddg.DrawDdgPanel: See initiator docstring.
• schrodinger.application.mcpro.fep.DrawFepPanel: See initiator docstring.
• schrodinger.application.mcpro.lrm.DrawLrmPanel: See initiator docstring.
• schrodinger.application.mcpro.mc.DrawMcPanel: See initiator docstring.
• schrodinger.application.mcpro.mini.DrawMiniPanel: See initiator docstring.
• schrodinger.application.mcpro.solvent.DrawSolventPanel
• schrodinger.project.EmptyIterator: Empty iterator.
• schrodinger.application.desmond.energygroup.EnergyComponent: Class for storing different energy components.
• schrodinger.application.desmond.energygroup.EnergyGroupAnalysis
• schrodinger.trajectory.ffstructure.FFStructure: A class containing force field information.
• schrodinger.application.bioluminate.actions.factory.Factory: A class dedicated to the creation, deletion and modification of groups of actions.
• schrodinger.application.glide.glide.FeaturePattern: Class defining a constraint feature pattern.
• schrodinger.structutils.smilesfilter.FilterReporter: A class to handle reporting of results from the remove_dupes function.
• schrodinger.analysis.enrichment.FingerprintFromFileGenerator: Class to generate (identifier, fingerprint) items, one at a time, from a structure file.
• schrodinger.application.lid.lid2d.intervaltree2d.FirstSecondaryStructure
• schrodinger.application.glide.newxp_reorg_fit.FitNewxpReorgEnergy: Helper class to fit the newXP reorganization energy
• schrodinger.application.prime.primefix.FixForPrime: Wrapper class to house the combination of methods for fixing a structure for Prime.
• schrodinger.application.desmond.fep_gui.FragClass: Class for storing the data for each fragment row.
• schrodinger.application.desmond.gaussian_filter.GaussianFilter
• Tkinter.Grid: Geometry manager Grid.
  • Tkinter.Widget: Internal class.
    • Tkinter.Button: Button widget.
      • schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
        • schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
      • schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
    • Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
      • schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
        • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
    • Tkinter.Checkbutton: Checkbutton widget which is either in on- or off-state.
      • schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
        • schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
      • schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
        • schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
        • schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
    • Tkinter.Entry: Entry widget which allows to display simple text.
      • schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
      • schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
    • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
      • schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
        • schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
        • schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
        • schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
        • schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
          • schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
          • schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
        • schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
        • schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
        • schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
        • schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
        • schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
        • schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
        • schrodinger.application.desmond.table._TableWidget: A base class for all Table* widget classes except the Table class.
          • schrodinger.application.desmond.table.TableButton: Defines a button widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableCheckbutton: Defines a check-button widget (similar to the Tkinter one) upon _TableWidget.
          • schrodinger.application.desmond.table.TableComboBox: Defines a ComboBox widget (similar to 'Pmw.ComboBox') upon _TableWidget.
          • schrodinger.application.desmond.table.TableEntry: Defines a entry widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableEntryField: Defines a entry widget (similar to 'Pmw.EntryField') upon _TableWidget.
          • schrodinger.application.desmond.table.TableLabel: Defines a label widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableRadiobutton: Defines a radio-button widget (similar to the Tkinter one) upon _TableWidget.
          • schrodinger.application.desmond.table.TableSpinbox: Defines a spin box widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableTextButton: Defines a text-button widget upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableTitle: Defines a Button widget (similar to the Tkinter one) upon '_TableWidget'.
      • schrodinger.ui.widget.tkinterwidget.HorizontalBar: Class intended to mimic the horizontal bar that divides the bottom buttons from the rest of the panel in Maestro.
      • schrodinger.ui.multilistbox.MultiListbox: A Frame containing a table-like, column sortable, scrollable, list boxes.
    • Tkinter.Label: Label widget which can display text and bitmaps.
      • schrodinger.ui.widget.tkinterwidget.Label: Class that mimics the Tkinter.Label class.
        • schrodinger.ui.widgettable.LabelCell: Subclass of Tkinter Label widget and Cell.
    • Tkinter.LabelFrame: labelframe widget.
      • schrodinger.ui.widget.tkinterwidget.LabelFrame: Class that mimics the Tkinter.LabelFrame class.
    • Tkinter.Listbox: Listbox widget which can display a list of strings.
      • schrodinger.ui.widget.tkinterwidget.Listbox: Class that mimics the Tkinter.Listbox class.
    • Tkinter.Menu: Menu widget which allows to display menu bars, pull-down menus and pop-up menus.
      • schrodinger.ui.widget.tkinterwidget.Menu: Class that mimics the Tkinter.Menu class.
    • Tkinter.Menubutton: Menubutton widget, obsolete since Tk8.0.
      • schrodinger.ui.widget.tkinterwidget.Menubutton: Class that mimics the Tkinter.Menubutton class.
    • Tkinter.Message: Message widget to display multiline text.
      • schrodinger.ui.widget.tkinterwidget.Message: Class that mimics the Tkinter.Message class.
    • Tkinter.PanedWindow: panedwindow widget.
      • schrodinger.ui.widget.tkinterwidget.PanedWindow: Class that mimics the Tkinter.PanedWindow class.
    • Tkinter.Radiobutton: Radiobutton widget which shows only one of several buttons in on-state.
      • schrodinger.ui.widget.tkinterwidget.Radiobutton: Class that mimics the Tkinter.Radiobutton class.
        • schrodinger.ui.widgettable.RadiobuttonCell: Subclass of Tkinter Radiobutton widget and Cell.
    • Tkinter.Scale: Scale widget which can display a numerical scale.
      • schrodinger.ui.widget.tkinterwidget.Scale: Class that mimics the Tkinter.Scale class.
    • Tkinter.Scrollbar: Scrollbar widget which displays a slider at a certain position.
      • schrodinger.ui.widget.tkinterwidget.Scrollbar: Class that mimics the Tkinter.Scrollbar class.
    • Tkinter.Spinbox: spinbox widget.
      • schrodinger.ui.widget.tkinterwidget.Spinbox: Class that mimics the Tkinter.Spinbox class.
        • schrodinger.application.desmond.table.TableSpinbox._Spinbox
    • Tkinter.Text: Text widget which can display text in various forms.
      • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
      • schrodinger.application.desmond.table.TextButton
• schrodinger.ui.widget.tkinterwidget.GroundClass: Necessary method for "grounding" all of the pick toggle preset methods in the event that the GUI is run outside of Maestro (Since pick toggles are used for choosing molecules, etc.
  • schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
    • schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
    • schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
• schrodinger.protein.findhets.GroupByConnectivity: Groups the atoms by molecule connectivity.
• schrodinger.application.desmond.mdkey.GuiMap
• urllib2.HTTPPasswordMgr
  • schrodinger.utils.urllib.ProxyPasswordManager
    • schrodinger.utils.urllib.ProxyPasswordManagerQt: A password manager sub-class that uses Qt to post a dialog to request the password.
• optparse.HelpFormatter: Abstract base class for formatting option help.
  • optparse.IndentedHelpFormatter: Format help with indented section bodies.
    • schrodinger.utils.cmdline.DelegatingIndentedHelpFormatter: An IndentedHelpFormatter class that allows an Option class to alter its own option string if it has a process_option_strings method.
• Tkinter.Image: Base class for images.
  • Tkinter.PhotoImage: Widget which can display colored images in GIF, PPM/PGM format.
    • schrodinger.ui.widget.tkinterwidget.PhotoImage: Class that mimics the Tkinter.PhotoImage class.
• schrodinger.application.mcpro.read_output.ImportSumfile: Method to read all data from current summary/monitor file and return the status and properties of interest in a hash.
• schrodinger.application.lid.lid2d.intervaltree2d.IntervalTree
• schrodinger.application.lid.lid2d.intervaltree2d.IntervalTreeNode
• schrodinger.ui.qt.appframework.JobParameters: Class for holding job parameters.
• schrodinger.ui.appframework.JobParameters: Class for holding job parameters.
• schrodinger.job.launcher.Launcher: Run a program (typically a Python or shell script) under job control.
• schrodinger.application.lid.ligand_interaction_diagram.LigandInteractionDiagram
• schrodinger.infra.mmim.MMIMArgList: A class to provide list-like access to MMIM array properties.
• _Pmw.Pmw_1_2.lib.PmwBase.MegaArchetype
  • _Pmw.Pmw_1_2.lib.PmwMainMenuBar.MainMenuBar
    • schrodinger.ui.widget.pmwwidget.MainMenuBar: Class that mimics the Pmw.MainMenuBar class.
  • _Pmw.Pmw_1_2.lib.PmwBase.MegaToplevel
    • _Pmw.Pmw_1_2.lib.PmwBalloon.Balloon
      • schrodinger.ui.widget.pmwwidget.Balloon: Class that mimics the Pmw.Balloon class.
    • schrodinger.ui.widget._private._enhancedDialog
      • schrodinger.ui.widget.pmwwidget.Dialog: Class that mimics the Pmw.Dialog class.
      • schrodinger.ui.widget._private._enhancedMessageDialog
        • schrodinger.ui.widget.pmwwidget.MessageDialog: Class that mimics the Pmw.Dialog class.
          • schrodinger.ui.widget.pmwwidget.showinfo: Class designed to mimic the tkMessageBox.showinfo class with the caveat that a parent argument must be specified.
          • schrodinger.ui.widget.pmwwidget.showwarning: Class designed to mimic the tkMessageBox.showwarning class with the caveat that a parent argument must be specified.
      • schrodinger.ui.widget._private._enhancedPromptDialog
        • schrodinger.ui.widget.pmwwidget.PromptDialog: Class that mimics the Pmw.Dialog class.
  • _Pmw.Pmw_1_2.lib.PmwBase.MegaWidget
    • _Pmw.Pmw_1_2.lib.PmwButtonBox.ButtonBox
      • schrodinger.ui.widget.pmwwidget.ButtonBox: Class that mimics the Pmw.ButtonBox class.
    • _Pmw.Pmw_1_2.lib.PmwGroup.Group
      • schrodinger.ui.widget.pmwwidget.Group: Class that mimics the Pmw.Group class.
    • _Pmw.Pmw_1_2.lib.PmwOptionMenu.OptionMenu
      • schrodinger.ui.widget.pmwwidget.OptionMenu: Class that mimics the Pmw.OptionMenu class.
        • schrodinger.ui.widgettable.OptionMenuCell: Subclass of Tkinter OptionMenu and Cell.
    • _Pmw.Pmw_1_2.lib.PmwRadioSelect.RadioSelect
      • schrodinger.ui.widget.pmwwidget.RadioSelect: Class that mimics the Pmw.RadioSelect class.
    • _Pmw.Pmw_1_2.lib.PmwScrolledCanvas.ScrolledCanvas
      • schrodinger.ui.widget.pmwwidget.ScrolledCanvas: Class that mimics the Pmw.ScrolledCanvas class.
    • _Pmw.Pmw_1_2.lib.PmwScrolledText.ScrolledText
      • schrodinger.ui.widget.pmwwidget.ScrolledText: Class that mimics the Pmw.ScrolledText class.
    • schrodinger.ui.widgettable._ScrolledDouble: Two frames that are scrolled with one vertical scroll bar.
      • schrodinger.ui.widgettable.WidgetTable: The table class with scroll bars
    • schrodinger.ui.widget._private._fixedComboBox
      • schrodinger.ui.widget.pmwwidget.ComboBox: Class that mimics the Pmw.ComboBox class.
        • schrodinger.ui.propertyselector.PropertySelectorMenu: Pull-down menu style property selected Used by VSW GUI
        • schrodinger.application.desmond.table.TableComboBox._ComboBox
    • schrodinger.ui.widget._private._fixedCounter
      • schrodinger.ui.widget.pmwwidget.Counter: Class that mimics the Pmw.Counter class.
    • schrodinger.ui.widget._private._fixedEntryField
      • schrodinger.ui.widget.pmwwidget.EntryField: Class that mimics the Pmw.EntryField class.
        • schrodinger.ui.widgettable.EntryFieldCell: Subclass of Tkinter EntryField and Cell.
        • schrodinger.application.desmond.table.TableEntryField._EntryField
    • schrodinger.ui.widget._private._fixedPanedWidget
      • schrodinger.ui.widget.pmwwidget.PanedWidget: Class that mimics the Pmw.PanedWidget class.
    • schrodinger.ui.widget._private._fixedScrolledFrame
      • schrodinger.ui.widget.pmwwidget.ScrolledFrame: Class that mimics the Pmw.ScrolledFrame class.
        • schrodinger.application.desmond.table.Table: A table widget class.
    • schrodinger.ui.widget._private._fixedScrolledListBox
      • schrodinger.ui.widget.pmwwidget.ScrolledListBox: Class that mimics the Pmw.ScrolledListBox class.
  • schrodinger.ui.widget._private._roundNoteBook
    • schrodinger.ui.widget.pmwwidget.NoteBook: Class that mimics the Pmw.NoteBook class.
• schrodinger.protein.membrane.Membrane_Model
• schrodinger.application.desmond.meta.Meta
• schrodinger.application.desmond.meta.MetaDynamicsAnalysis: Analysis tools for Desmond's metadynamics jobs.
• Tkinter.Misc: Internal class.
  • Tkinter.BaseWidget: Internal class.
    • Tkinter.Toplevel: Toplevel widget, e.g.
      • schrodinger.ui.widget.tkinterwidget.Toplevel: Class that mimics the Tkinter.Toplevel class.
    • Tkinter.Widget: Internal class.
      • Tkinter.Button: Button widget.
        • schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
          • schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
        • schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
      • Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
        • schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
          • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
      • Tkinter.Checkbutton: Checkbutton widget which is either in on- or off-state.
        • schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
          • schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
        • schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
          • schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
          • schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
      • Tkinter.Entry: Entry widget which allows to display simple text.
        • schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
        • schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
      • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
        • schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
          • schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
          • schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
          • schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
          • schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
            • schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
            • schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
          • schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
          • schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
          • schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
          • schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
          • schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
          • schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
          • schrodinger.application.desmond.table._TableWidget: A base class for all Table* widget classes except the Table class.
            • schrodinger.application.desmond.table.TableButton: Defines a button widget (similar to the Tkinter one) upon '_TableWidget'.
            • schrodinger.application.desmond.table.TableCheckbutton: Defines a check-button widget (similar to the Tkinter one) upon _TableWidget.
            • schrodinger.application.desmond.table.TableComboBox: Defines a ComboBox widget (similar to 'Pmw.ComboBox') upon _TableWidget.
            • schrodinger.application.desmond.table.TableEntry: Defines a entry widget (similar to the Tkinter one) upon '_TableWidget'.
            • schrodinger.application.desmond.table.TableEntryField: Defines a entry widget (similar to 'Pmw.EntryField') upon _TableWidget.
            • schrodinger.application.desmond.table.TableLabel: Defines a label widget (similar to the Tkinter one) upon '_TableWidget'.
            • schrodinger.application.desmond.table.TableRadiobutton: Defines a radio-button widget (similar to the Tkinter one) upon _TableWidget.
            • schrodinger.application.desmond.table.TableSpinbox: Defines a spin box widget (similar to the Tkinter one) upon '_TableWidget'.
            • schrodinger.application.desmond.table.TableTextButton: Defines a text-button widget upon '_TableWidget'.
            • schrodinger.application.desmond.table.TableTitle: Defines a Button widget (similar to the Tkinter one) upon '_TableWidget'.
        • schrodinger.ui.widget.tkinterwidget.HorizontalBar: Class intended to mimic the horizontal bar that divides the bottom buttons from the rest of the panel in Maestro.
        • schrodinger.ui.multilistbox.MultiListbox: A Frame containing a table-like, column sortable, scrollable, list boxes.
      • Tkinter.Label: Label widget which can display text and bitmaps.
        • schrodinger.ui.widget.tkinterwidget.Label: Class that mimics the Tkinter.Label class.
          • schrodinger.ui.widgettable.LabelCell: Subclass of Tkinter Label widget and Cell.
      • Tkinter.LabelFrame: labelframe widget.
        • schrodinger.ui.widget.tkinterwidget.LabelFrame: Class that mimics the Tkinter.LabelFrame class.
      • Tkinter.Listbox: Listbox widget which can display a list of strings.
        • schrodinger.ui.widget.tkinterwidget.Listbox: Class that mimics the Tkinter.Listbox class.
      • Tkinter.Menu: Menu widget which allows to display menu bars, pull-down menus and pop-up menus.
        • schrodinger.ui.widget.tkinterwidget.Menu: Class that mimics the Tkinter.Menu class.
      • Tkinter.Menubutton: Menubutton widget, obsolete since Tk8.0.
        • schrodinger.ui.widget.tkinterwidget.Menubutton: Class that mimics the Tkinter.Menubutton class.
      • Tkinter.Message: Message widget to display multiline text.
        • schrodinger.ui.widget.tkinterwidget.Message: Class that mimics the Tkinter.Message class.
      • Tkinter.PanedWindow: panedwindow widget.
        • schrodinger.ui.widget.tkinterwidget.PanedWindow: Class that mimics the Tkinter.PanedWindow class.
      • Tkinter.Radiobutton: Radiobutton widget which shows only one of several buttons in on-state.
        • schrodinger.ui.widget.tkinterwidget.Radiobutton: Class that mimics the Tkinter.Radiobutton class.
          • schrodinger.ui.widgettable.RadiobuttonCell: Subclass of Tkinter Radiobutton widget and Cell.
      • Tkinter.Scale: Scale widget which can display a numerical scale.
        • schrodinger.ui.widget.tkinterwidget.Scale: Class that mimics the Tkinter.Scale class.
      • Tkinter.Scrollbar: Scrollbar widget which displays a slider at a certain position.
        • schrodinger.ui.widget.tkinterwidget.Scrollbar: Class that mimics the Tkinter.Scrollbar class.
      • Tkinter.Spinbox: spinbox widget.
        • schrodinger.ui.widget.tkinterwidget.Spinbox: Class that mimics the Tkinter.Spinbox class.
          • schrodinger.application.desmond.table.TableSpinbox._Spinbox
      • Tkinter.Text: Text widget which can display text in various forms.
        • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
        • schrodinger.application.desmond.table.TextButton
  • Tkinter.Tk: Toplevel widget of Tk which represents mostly the main window of an appliation.
    • schrodinger.ui.widget.tkinterwidget.Tk: This is a Schrodinger-ized Tk instance.
      • schrodinger.ui.appframework.AppFramework: The AppFramework class is basically a hull for applications.
• schrodinger.trajectory.rmsd2d.ModelBase
  • schrodinger.trajectory.rmsd2d.MultiprocessingModel
  • schrodinger.trajectory.rmsd2d.ThreadingModel
• schrodinger.application.mcpro.modelsystemwizard.ModelSystem: This is where all information regarding the model system are stored.
• schrodinger.application.mcpro.modelsystemwizard.ModelSystemPanel: Class to draw the model-system-creation panel
• schrodinger.structutils.io.MultiFileReader: Reads structures from multiple files.
• schrodinger.structutils.io.MultiFileWriter: Writes structres to basename-NNN<extension> while never writing more than 100,000 structures to a file.
• schrodinger.application.desmond.fep_gui.MutClass: Class for storing the data for each mutation row.
• schrodinger.application.bioluminate.protein.Mutation: Helper class for Mutator.
• schrodinger.application.bioluminate.protein.Mutator: Mutates a set of residues in a protein structure allowing concurrent mutations as well as the option to limit concurrent mutations to sequential residues only.
• optparse.Option: Instance attributes: _short_opts : [string] _long_opts : [string]
  • schrodinger.utils.cmdline.SingleDashOption: A class to automatically translate long options with single dashes into double dash long options, but still print out help with the single dash.
• optparse.OptionContainer: Abstract base class.
  • optparse.OptionParser: Class attributes: standard_option_list : [Option] list of standard options that will be accepted by all instances of this parser class (intended to be overridden by subclasses).
    • schrodinger.utils.cmdline.SingleDashOptionParser: An OptionParser subclass that allows long options with a single dash.
• Tkinter.Pack: Geometry manager Pack.
  • Tkinter.Widget: Internal class.
    • Tkinter.Button: Button widget.
      • schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
        • schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
      • schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
    • Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
      • schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
        • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
    • Tkinter.Checkbutton: Checkbutton widget which is either in on- or off-state.
      • schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
        • schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
      • schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
        • schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
        • schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
    • Tkinter.Entry: Entry widget which allows to display simple text.
      • schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
      • schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
    • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
      • schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
        • schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
        • schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
        • schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
        • schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
          • schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
          • schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
        • schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
        • schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
        • schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
        • schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
        • schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
        • schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
        • schrodinger.application.desmond.table._TableWidget: A base class for all Table* widget classes except the Table class.
          • schrodinger.application.desmond.table.TableButton: Defines a button widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableCheckbutton: Defines a check-button widget (similar to the Tkinter one) upon _TableWidget.
          • schrodinger.application.desmond.table.TableComboBox: Defines a ComboBox widget (similar to 'Pmw.ComboBox') upon _TableWidget.
          • schrodinger.application.desmond.table.TableEntry: Defines a entry widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableEntryField: Defines a entry widget (similar to 'Pmw.EntryField') upon _TableWidget.
          • schrodinger.application.desmond.table.TableLabel: Defines a label widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableRadiobutton: Defines a radio-button widget (similar to the Tkinter one) upon _TableWidget.
          • schrodinger.application.desmond.table.TableSpinbox: Defines a spin box widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableTextButton: Defines a text-button widget upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableTitle: Defines a Button widget (similar to the Tkinter one) upon '_TableWidget'.
      • schrodinger.ui.widget.tkinterwidget.HorizontalBar: Class intended to mimic the horizontal bar that divides the bottom buttons from the rest of the panel in Maestro.
      • schrodinger.ui.multilistbox.MultiListbox: A Frame containing a table-like, column sortable, scrollable, list boxes.
    • Tkinter.Label: Label widget which can display text and bitmaps.
      • schrodinger.ui.widget.tkinterwidget.Label: Class that mimics the Tkinter.Label class.
        • schrodinger.ui.widgettable.LabelCell: Subclass of Tkinter Label widget and Cell.
    • Tkinter.LabelFrame: labelframe widget.
      • schrodinger.ui.widget.tkinterwidget.LabelFrame: Class that mimics the Tkinter.LabelFrame class.
    • Tkinter.Listbox: Listbox widget which can display a list of strings.
      • schrodinger.ui.widget.tkinterwidget.Listbox: Class that mimics the Tkinter.Listbox class.
    • Tkinter.Menu: Menu widget which allows to display menu bars, pull-down menus and pop-up menus.
      • schrodinger.ui.widget.tkinterwidget.Menu: Class that mimics the Tkinter.Menu class.
    • Tkinter.Menubutton: Menubutton widget, obsolete since Tk8.0.
      • schrodinger.ui.widget.tkinterwidget.Menubutton: Class that mimics the Tkinter.Menubutton class.
    • Tkinter.Message: Message widget to display multiline text.
      • schrodinger.ui.widget.tkinterwidget.Message: Class that mimics the Tkinter.Message class.
    • Tkinter.PanedWindow: panedwindow widget.
      • schrodinger.ui.widget.tkinterwidget.PanedWindow: Class that mimics the Tkinter.PanedWindow class.
    • Tkinter.Radiobutton: Radiobutton widget which shows only one of several buttons in on-state.
      • schrodinger.ui.widget.tkinterwidget.Radiobutton: Class that mimics the Tkinter.Radiobutton class.
        • schrodinger.ui.widgettable.RadiobuttonCell: Subclass of Tkinter Radiobutton widget and Cell.
    • Tkinter.Scale: Scale widget which can display a numerical scale.
      • schrodinger.ui.widget.tkinterwidget.Scale: Class that mimics the Tkinter.Scale class.
    • Tkinter.Scrollbar: Scrollbar widget which displays a slider at a certain position.
      • schrodinger.ui.widget.tkinterwidget.Scrollbar: Class that mimics the Tkinter.Scrollbar class.
    • Tkinter.Spinbox: spinbox widget.
      • schrodinger.ui.widget.tkinterwidget.Spinbox: Class that mimics the Tkinter.Spinbox class.
        • schrodinger.application.desmond.table.TableSpinbox._Spinbox
    • Tkinter.Text: Text widget which can display text in various forms.
      • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
      • schrodinger.application.desmond.table.TextButton
• schrodinger.application.desmond.energygroup.PairDict: PairDict is a special dictionary that treats pairs with the same element as equals, independent of order.
• schrodinger.application.mcpro.perturbations.PertID: Storage class for perturbation identification
• schrodinger.application.mcpro.perturbations.PertReorder: Storage class for perturbation reordering
• schrodinger.application.mcpro.perturbations.Perturbations: Class to read, create, and manipulate the graph of perturbations from which user-specified list of fragments will be converted to a list of FEPs to be run
• schrodinger.pipeline.pipeio.PipeIO: Parent class for all Pipeline I/O classes.
  • schrodinger.pipeline.pipeio.Grid: A class to hold a set of grid files (compressed or uncompressed).
  • schrodinger.pipeline.pipeio.PhaseDB: A class to hold the absolute pathname of a Phase database.
  • schrodinger.pipeline.pipeio.Structures: A class to hold the names of structure files.
  • schrodinger.pipeline.pipeio.Text: A class to hold the names of one or more text (or log) files.
• schrodinger.pipeline.pipeline.Pipeline: A controller responsible for running the stages in the correct order.
• Tkinter.Place: Geometry manager Place.
  • Tkinter.Widget: Internal class.
    • Tkinter.Button: Button widget.
      • schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
        • schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
      • schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
    • Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
      • schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
        • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
    • Tkinter.Checkbutton: Checkbutton widget which is either in on- or off-state.
      • schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
        • schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
      • schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
        • schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
        • schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
    • Tkinter.Entry: Entry widget which allows to display simple text.
      • schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
      • schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
    • Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
      • schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
        • schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
        • schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
        • schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
        • schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
          • schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
          • schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
        • schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
        • schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
        • schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
        • schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
        • schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
        • schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
        • schrodinger.application.desmond.table._TableWidget: A base class for all Table* widget classes except the Table class.
          • schrodinger.application.desmond.table.TableButton: Defines a button widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableCheckbutton: Defines a check-button widget (similar to the Tkinter one) upon _TableWidget.
          • schrodinger.application.desmond.table.TableComboBox: Defines a ComboBox widget (similar to 'Pmw.ComboBox') upon _TableWidget.
          • schrodinger.application.desmond.table.TableEntry: Defines a entry widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableEntryField: Defines a entry widget (similar to 'Pmw.EntryField') upon _TableWidget.
          • schrodinger.application.desmond.table.TableLabel: Defines a label widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableRadiobutton: Defines a radio-button widget (similar to the Tkinter one) upon _TableWidget.
          • schrodinger.application.desmond.table.TableSpinbox: Defines a spin box widget (similar to the Tkinter one) upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableTextButton: Defines a text-button widget upon '_TableWidget'.
          • schrodinger.application.desmond.table.TableTitle: Defines a Button widget (similar to the Tkinter one) upon '_TableWidget'.
      • schrodinger.ui.widget.tkinterwidget.HorizontalBar: Class intended to mimic the horizontal bar that divides the bottom buttons from the rest of the panel in Maestro.
      • schrodinger.ui.multilistbox.MultiListbox: A Frame containing a table-like, column sortable, scrollable, list boxes.
    • Tkinter.Label: Label widget which can display text and bitmaps.
      • schrodinger.ui.widget.tkinterwidget.Label: Class that mimics the Tkinter.Label class.
        • schrodinger.ui.widgettable.LabelCell: Subclass of Tkinter Label widget and Cell.
    • Tkinter.LabelFrame: labelframe widget.
      • schrodinger.ui.widget.tkinterwidget.LabelFrame: Class that mimics the Tkinter.LabelFrame class.
    • Tkinter.Listbox: Listbox widget which can display a list of strings.
      • schrodinger.ui.widget.tkinterwidget.Listbox: Class that mimics the Tkinter.Listbox class.
    • Tkinter.Menu: Menu widget which allows to display menu bars, pull-down menus and pop-up menus.
      • schrodinger.ui.widget.tkinterwidget.Menu: Class that mimics the Tkinter.Menu class.
    • Tkinter.Menubutton: Menubutton widget, obsolete since Tk8.0.
      • schrodinger.ui.widget.tkinterwidget.Menubutton: Class that mimics the Tkinter.Menubutton class.
    • Tkinter.Message: Message widget to display multiline text.
      • schrodinger.ui.widget.tkinterwidget.Message: Class that mimics the Tkinter.Message class.
    • Tkinter.PanedWindow: panedwindow widget.
      • schrodinger.ui.widget.tkinterwidget.PanedWindow: Class that mimics the Tkinter.PanedWindow class.
    • Tkinter.Radiobutton: Radiobutton widget which shows only one of several buttons in on-state.
      • schrodinger.ui.widget.tkinterwidget.Radiobutton: Class that mimics the Tkinter.Radiobutton class.
        • schrodinger.ui.widgettable.RadiobuttonCell: Subclass of Tkinter Radiobutton widget and Cell.
    • Tkinter.Scale: Scale widget which can display a numerical scale.
      • schrodinger.ui.widget.tkinterwidget.Scale: Class that mimics the Tkinter.Scale class.
    • Tkinter.Scrollbar: Scrollbar widget which displays a slider at a certain position.
      • schrodinger.ui.widget.tkinterwidget.Scrollbar: Class that mimics the Tkinter.Scrollbar class.
    • Tkinter.Spinbox: spinbox widget.
      • schrodinger.ui.widget.tkinterwidget.Spinbox: Class that mimics the Tkinter.Spinbox class.
        • schrodinger.application.desmond.table.TableSpinbox._Spinbox
    • Tkinter.Text: Text widget which can display text in various forms.
      • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
      • schrodinger.application.desmond.table.TextButton
• schrodinger.application.desmond.gui.PosResRow
• schrodinger.application.glide.glideanalysis.PoseLibrary: A helper class to sort a pose library.
• schrodinger.application.bioluminate.protein.PrimeStructure
• schrodinger.application.prime.packages.PrimeStructureDatabase.PrimeStructureDB
  • schrodinger.antibody_db_manage_gui.OrderedDB: Adds a method to the parent class psd.PrimeStructureDB to return all the values in a column ordered by a specific key
• schrodinger.ui.qt.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
  • schrodinger.application.bioluminate.propfilter.PropertySelectorWithRanges: A PropertySelector class that appends ranges to the names of numeric properties.
• schrodinger.protein.assignment.ProtAssign
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QFileDialog
• PyQt4.QtGui.QWidget
• schrodinger.trajectory.rmsd2d.RMSDCalculator: A multi-threading class to calculat pairwise RMSD on a set of trajectory frames.
  • schrodinger.trajectory.rmsd2d.RMSDMultiprocessing
  • schrodinger.trajectory.rmsd2d.RMSDThreading
• schrodinger.ui.qt.rama.Rama: A class showing a matplotlib plot of the Phi and Psi angles in a helix
  • schrodinger.application.bioluminate.protein_structure_quality.HomologyRama: A Ramachandran plot customized for the Protein Structure Quality Viewer
• schrodinger.ui.rama.Rama
• schrodinger.ui.appframework.ReadDialog: Dialog allowing user to specify a file to read in.
• schrodinger.ui.qt.appframework.ReadDialog: Dialog allowing user to specify a file to read in.
• schrodinger.application.bioluminate.protein.Refiner: Creates input files and runs calculations for protein refinement jobs using Prime and our schrodinger.structutils.minimize.Minimizer class.
• schrodinger.application.glide.newxp_reorg_fit.ReorgFitting: Class to compile input data appropriate for fitting and execute various fits of XP Reorg term to experiemntal data
• schrodinger.protein.analysis.Report: A class to calculate properties of proteins.
• schrodinger.application.report2d.Report2D
• schrodinger.application.mcpro.residuetools.ResidueTools: Class with tools to help in manipulating proteins
• schrodinger.infra.mm.ReturnCode: A class to hold special return code values and translate return code values into names.
• schrodinger.ui.widgettable.RowIterator: table.row Class for iterating over rows and for getting a row object Ex: row = table.row[rowid]
• schrodinger.application.macromodel.utils.SbcUtil: A class for writing substructure/constraint files to accompany jobname.com.
• schrodinger.application.lid.lid2d.intervaltree2d.SecondSecondaryStructure
• schrodinger.protein.sequence.Sequence: Class representing a sequence of protein residues.
• schrodinger.structutils.sitealign.SiteMatchLookup: Lookup for any reference and mobile structures that have matching binding site atoms.
• schrodinger.structutils.smilesfilter.SmilesErrorHandler: A class that acts as an error handler for cases where SMILES generation fails.
• schrodinger.structutils.smiles.SmilesGenerator: A class to generate a SMILES string from a Structure object.
• schrodinger.pipeline.stage.StageInput: Class defining a stage input
• schrodinger.pipeline.pipeline.StageJob: A "Job" that is used by Pipeline to run a Stage.
• schrodinger.pipeline.stage.StageOutput: Class defining a stage output
• schrodinger.ui.appframework.StartDialog: Toplevel Tkinter widget that mimics the Maestro Start dialog.
• schrodinger.ui.qt.appframework.StartDialog: Toplevel Qt widget that mimics the Maestro Start dialog.
• schrodinger.analysis.enrichment.StatisticalSummary: Container class to store summary metrics describing an array of numerical values.
• schrodinger.structutils.sort.StructureFileSorter: A class to sort structure files by ct-level property values.
• schrodinger.application.combiglide.corehop.SubstCoreDatabase: This class can be used to calculate substitution scores, where a core hopping database has been used to generate passed ligands.
• schrodinger.application.desmond.system_builder_inp.SystemBuilderInput
• schrodinger.infra.table.TableRow: This class represents a table row--what you get by indexing a Table.
• schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer: Summarize the similarity differences within and between two groups of fingerprints.
• UserDict.UserDict
  • UserDict.IterableUserDict
    • schrodinger.pipeline.stage.Stage
      • schrodinger.pipeline.stages.filtering.ChargeFilterStage: Stage-based class for filtering a set of structure files by total charge.
      • schrodinger.pipeline.stages.combine.CombineStage: Stage for combining multiple Structures objects into one.
      • schrodinger.pipeline.stages.macromodel.ConfSearchStage: Stage for running MacroModel calculations
      • schrodinger.pipeline.stages.convert.ConvertStage: Stage for converting structure files from one format to another Each file is converted using Schrodingers specific conversion utility and the number of files is not changed.
      • schrodinger.pipeline.stages.phase.DBConfSitesStage: Stage for generating conformations for structures in a Phase database.
      • schrodinger.pipeline.stages.phase.DBExportStage: Stage for exporting structures from a Phase database.
      • schrodinger.pipeline.stages.phase.DBManageStage: Stage for creating a Phase database.
      • schrodinger.pipeline.stages.glide.DockingStage: VSW stage for performing Glide docking
      • schrodinger.pipeline.stages.filtering.DrugLikeSplitStage: Stage for splitting the input ligand structures into 3 groups:
      • schrodinger.pipeline.stages.gencodes.GenCodesStage: Stage for generating compound and variant codes, which are stored as properties.
      • schrodinger.pipeline.stages.combine.GenerateCovalentComplexesStage: Stage for combining specified receptor with specified ligands via covalent bond to form complexes.
      • schrodinger.pipeline.stages.filtering.GeneratePropsStage: Ev:85070
      • schrodinger.pipeline.stages.glide.GlideSortStage: Stage for sorting Glide _pv/lib.mae files.
      • schrodinger.pipeline.stages.glide.GridgenStage
      • schrodinger.pipeline.stages.filtering.LigFilterStage: Stage interface for the LigFilter utility.
      • schrodinger.pipeline.stages.ligprep.LigPrepStage: Pipeline stage for running LigPrep on the input structures
      • schrodinger.pipeline.stages.prime.MMGBSAStage: Stage for running Prime MM-GBSA on input structures.
      • schrodinger.pipeline.stages.filtering.MergeDuplicatesStage: Stage for removing duplicate variants within each root (compound) based on unique SMILES strings.
      • schrodinger.pipeline.stages.glide.MergeStage: Stage for merging up to 100 Glide output files with 'glide_ensemble_merge'.
      • schrodinger.pipeline.stages.ligprep.PostLigPrepStage: This stage limits the number of steroisomers, removes states penalized by Epik/Ionizer, and generates the variant codes.
      • schrodinger.pipeline.stages.prime.PrimeStage: Prime Active Site Optimization stage: Performs the familiar sidechain prediction plus minimization, used by IFD jobs.
      • schrodinger.pipeline.stages.pull.PullStage: Stage for extracting a subset of ligands/compounds (and their variants) from a second set of ligand files, given the number or percent to keep from a first set of ligand files.
      • schrodinger.pipeline.stages.qsite.QSiteStage: Stage for running QSite jobs.
      • schrodinger.pipeline.stages.qikprop.QikPropStage: Stage for running QikProp jobs.
      • schrodinger.pipeline.stages.gencodes.RestoreTitlesStage: Stage for copying titles for each input ligand from the 's_pipeline_title_backup' property to the 's_m_title' property.
      • schrodinger.pipeline.stages.rmsd.RmsdStage: Stage for calculating RMSDs for structures in two sets.
      • schrodinger.pipeline.stages.macromodel.SampleRingsStage: Stage for sampling rings with 7 or more members using MacroModel
      • schrodinger.pipeline.stages.semiemp.SemiEmpStage: Stage for running semi-empirical jobs.
      • schrodinger.pipeline.stages.filtering.SubSetStage: Stage for making a subset of the input files based on a list of titles or other property.
• schrodinger.application.vsw.vswinput.VSWWriter: Use writeInputFile() method
• Tkinter.Variable: Class to define value holders for e.g.
  • Tkinter.BooleanVar: Value holder for boolean variables.
    • schrodinger.ui.widget.tkinterwidget.BooleanVar: Class that mimics the Tkinter.BooleanVar class.
  • Tkinter.DoubleVar: Value holder for float variables.
    • schrodinger.ui.widget.tkinterwidget.DoubleVar: Class that mimics the Tkinter.DoubleVar class.
  • Tkinter.IntVar: Value holder for integer variables.
    • schrodinger.ui.widget.tkinterwidget.IntVar: Class that mimics the Tkinter.IntVar class.
  • Tkinter.StringVar: Value holder for strings variables.
    • schrodinger.ui.widget.tkinterwidget.StringVar: Class that mimics the Tkinter.StringVar class.
• schrodinger.application.watermap.watermap_inp.WaterMapInput
• Tkinter.Wm: Provides functions for the communication with the window manager.
  • Tkinter.Tk: Toplevel widget of Tk which represents mostly the main window of an appliation.
    • schrodinger.ui.widget.tkinterwidget.Tk: This is a Schrodinger-ized Tk instance.
      • schrodinger.ui.appframework.AppFramework: The AppFramework class is basically a hull for applications.
  • Tkinter.Toplevel: Toplevel widget, e.g.
    • schrodinger.ui.widget.tkinterwidget.Toplevel: Class that mimics the Tkinter.Toplevel class.
• schrodinger.ui.qt.appframework.WriteDialog: Toplevel Qt widget that mimics the Write dialog.
• schrodinger.ui.appframework.WriteDialog: Toplevel Tkinter widget that mimics the Write dialog.
• schrodinger.application.mcpro.writeinputs.WriteInputs
• schrodinger.pipeline.input.Writer: Class for writing pipeline input files.
  • schrodinger.pipeline.input.LinearWriter: Class for writing linear stage maps (ones with no branches).
• Tkinter.XView: Mix-in class for querying and changing the horizontal position of a widget's window.
  • Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
    • schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
      • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
  • Tkinter.Entry: Entry widget which allows to display simple text.
    • schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
    • schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
  • Tkinter.Listbox: Listbox widget which can display a list of strings.
    • schrodinger.ui.widget.tkinterwidget.Listbox: Class that mimics the Tkinter.Listbox class.
  • Tkinter.Spinbox: spinbox widget.
    • schrodinger.ui.widget.tkinterwidget.Spinbox: Class that mimics the Tkinter.Spinbox class.
      • schrodinger.application.desmond.table.TableSpinbox._Spinbox
  • Tkinter.Text: Text widget which can display text in various forms.
    • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
    • schrodinger.application.desmond.table.TextButton
• schrodinger.application.glide.xpdes.XpDesReader: Class for parsing XP descriptor (.xpdes) files Written by Rajorshi Biswas Original version was not parsing the first line correctly (it was assuing the title is an integer).
• schrodinger.application.glide.xpdes.XpDesWriter
• Tkinter.YView: Mix-in class for querying and changing the vertical position of a widget's window.
  • Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
    • schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
      • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
  • Tkinter.Listbox: Listbox widget which can display a list of strings.
    • schrodinger.ui.widget.tkinterwidget.Listbox: Class that mimics the Tkinter.Listbox class.
  • Tkinter.Text: Text widget which can display text in various forms.
    • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
    • schrodinger.application.desmond.table.TextButton
• schrodinger.application.mcpro.zmat.Zmat: class to store a single Zmat and related objects
• schrodinger.application.mcpro.zmat.ZmatAddAng: Class to store additional angles
• schrodinger.application.mcpro.zmat.ZmatAddBnd: Class to store additional bonds
• schrodinger.application.mcpro.zmat.ZmatAddDih: Class to store additional dihedrals
• schrodinger.application.mcpro.zmat.ZmatAtom: class to store an atom of a zmat
• schrodinger.application.mcpro.zmat.ZmatBondAtomtypes: Class to store explicitly written stretch parameters
• schrodinger.application.mcpro.zmat.ZmatDomDef: Class to store domain definitions
• schrodinger.application.mcpro.zmat.ZmatGeoVar: class to store geometry variations
• schrodinger.application.mcpro.zmat.ZmatHarCons: Class to store harmonic constraints
• schrodinger.application.mcpro.zmat.ZmatNonBond: Class to store explicitly written non-bond parameters
• schrodinger.application.mcpro.zmat.ZmatVarDih: Class to store variable dihedrals
• schrodinger.project._AllRowsIterator: Iterator for all rows in the project or group
• schrodinger.application.desmond.fep_gui._Atom
• schrodinger.infra.mm._CCodeProfiler: A class for profiling the time spent in C functions.
• schrodinger.maestro.maestro._Callback: Class that allows each callback function to be registered by specifying it in the string format ("module.function") or in callable reference format (reference to function itself).
• schrodinger.ui.widgettable._Cell: Class defining a cell.
  • schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
  • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
  • schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
  • schrodinger.ui.widgettable.EntryFieldCell: Subclass of Tkinter EntryField and Cell.
  • schrodinger.ui.widgettable.LabelCell: Subclass of Tkinter Label widget and Cell.
  • schrodinger.ui.widgettable.OptionMenuCell: Subclass of Tkinter OptionMenu and Cell.
  • schrodinger.ui.widgettable.RadiobuttonCell: Subclass of Tkinter Radiobutton widget and Cell.
• schrodinger.trajectory.desmondsimulation._DesmondFrame: _DesmondFrame contains simulation data at a particular time.
• schrodinger.project._EntryGroupIterator: Iterator for entry groups in the project
• schrodinger.project._EntrySurfaceIterator: An iterator for the surfaces associated with a given entry.
• schrodinger.trajectory.ffstructure._FFAngleIterator
• schrodinger.trajectory.ffstructure._FFBondIterator
• schrodinger.trajectory.ffstructure._FFConstraintIterator
• schrodinger.trajectory.ffstructure._FFDihedralIterator
• schrodinger.trajectory.ffstructure._FFExclusionIterator
• schrodinger.trajectory.ffstructure._FFPairIterator
• schrodinger.trajectory.ffstructure._FFPseudoIterator
• schrodinger.trajectory.ffstructure._FFRestraintIterator
• schrodinger.trajectory.ffstructure._FFSiteIterator
• schrodinger.trajectory.ffstructure._FFVdwtypeIterator
• schrodinger.trajectory.ffstructure._FFVirtualIterator
• schrodinger.trajectory.desmondsimulation._FepTrajectory._FepFrame
• schrodinger.trajectory.desmondsimulation._FepTrajectory
• schrodinger.application.desmond.energygroup._Group
• schrodinger.application.phase.hypothesis._HypothesisFeature: Class representing a hypothesis feature.
• schrodinger.project._IncludedRowsIterator: Iterator for included rows of the project or group
• schrodinger.application.desmond.table._Index: An instance of this class is a callable object that returns the current index of the element in a list.
• schrodinger.trajectory.analyze_trajectories._KeywordProcessor: This class processes ARK keywords coming from a .st2 input file, it turns the keywords into Analysis objects to be used by the backend.
• schrodinger.utils.ligfilter._MySplit
• schrodinger.project._SelectedRowsIterator: Iterator for selected rows of the project or group
• schrodinger.infra.mm._Wrapper: Class used to wrap a function from pymmlibs, checking the return code and raising an exception if it is not of the correct 'OK' enum value.
• schrodinger.application.glide.xpdes._XpDesBlock
• schrodinger.ui.qt.rama.Rama.backbone_dihedral
• schrodinger.ui.rama.Rama.backbone_dihedral
• schrodinger.protein.assignment.ProtAssign.changeable
  • schrodinger.protein.assignment.ProtAssign.amide_changeable
  • schrodinger.protein.assignment.ProtAssign.amine_changeable
  • schrodinger.protein.assignment.ProtAssign.carboxyl_changeable
  • schrodinger.protein.assignment.ProtAssign.histidine_changeable
  • schrodinger.protein.assignment.ProtAssign.rotatable_changeable
  • schrodinger.protein.assignment.ProtAssign.water_changeable
• schrodinger.protein.analysis.Report.data_set.data_point: Class that holds the data for each point in a data set
• schrodinger.protein.analysis.Report.data_set: Base class for all data sets.
  • schrodinger.protein.analysis.Report.Bfactor_data_set: Class to compute and hold data for B-Factors
  • schrodinger.protein.analysis.Report.Gfactor_summary_data_set: Class to compute and hold data for G-factor summaries of the Backbone and Sidechain dihedrals.
  • schrodinger.protein.analysis.Report.backbone_dihedral_data_set: Class to compute and hold data for Backbone Dihedrals
  • schrodinger.protein.analysis.Report.bond_angle_data_set: Class to compute and hold data for Bond Angle Deviations
  • schrodinger.protein.analysis.Report.bond_length_data_set: Class to compute and hold data for Bond Length Deviations
  • schrodinger.protein.analysis.Report.chirality_data_set: Class to compute and hold C-alpha chirality data
  • schrodinger.protein.analysis.Report.gamma_Bfactor_data_set: Class to compute and hold data for B-Factors of sidechain gamma atoms
  • schrodinger.protein.analysis.Report.improper_torsion_data_set: Class to compute and hold RMS data for improper torsions
  • schrodinger.protein.analysis.Report.missing_atoms_data_set: Class to compute and hold information on missing atoms
  • schrodinger.protein.analysis.Report.peptide_planarity_data_set: Class to compute and hold data for Peptide Planarity
  • schrodinger.protein.analysis.Report.sidechain_dihedral_data_set: Class to compute and hold data for Sidechain Dihedrals
  • schrodinger.protein.analysis.Report.sidechain_planarity_data_set: Class to compute and hold RMS data for planarity of sidechains
  • schrodinger.protein.analysis.Report.steric_clash_data_set: Class to compute and hold data for Steric Clashes.
• schrodinger.protein.assignment.ProtAssign.hbond_cluster
• schrodinger.application.glide.liaison_lsbd.liaison
• schrodinger.protein.analysis.Report.local_atom: Private class used to store atom information locally for speed
• schrodinger.protein.analysis.Report.local_protein: Private class used to store protein information locally for convenience
• schrodinger.protein.analysis.Report.local_residue: Private class used to store residue information locally for convenience
• object: The most base type
  • schrodinger.trajectory.analysistool.AnalysisTool: AnalysisTool is a base class for creating analyses of schrodinger.trajectory.desmondsimulation.DesmondSimulation objects.
    • schrodinger.trajectory.analysis.Angle: A tool to calculate angles between selected atom sets.
    • schrodinger.trajectory.analysis.AverageStructure: A tool to calculate average position over time for each atom in a set.
    • schrodinger.trajectory.analysis.CenterOfMass: A tool to calculate center of mass of selected atoms.
    • schrodinger.trajectory.analysis.CenterOfMotion: A tool to calculate center of motion of selected atoms.
    • schrodinger.trajectory.analysis.CovarianceMatrix: A tool to calculate covmatiant matrix.
    • schrodinger.trajectory.analysis.Dihedral: A tool to calculate dihedral angles from selected atom sets.
    • schrodinger.trajectory.analysis.Distance: A tool to calculate distances between selected atom sets.
    • schrodinger.application.desmond.energygroup.EnergyGroup: A tool to calculate group-group interaction.
    • schrodinger.trajectory.analysis.HydrogenBondFinder: A tool to find hydrogen bonds present between two sets of molecules.
    • schrodinger.trajectory.analysis.HydrogenBondTracker: A tool to track the state of hydrogen bonds between atom sets.
    • schrodinger.trajectory.analysis.PlanarAngle: A tool calculate inter-planar angles from selected atoms
    • schrodinger.trajectory.analysis.Position: A tool to track positions of atoms.
    • schrodinger.trajectory.analysis.RMSD: A tool to calculate Root Mean Square Deviation from reference positions.
    • schrodinger.trajectory.analysis.RMSF: A tool to calculate Root Mean Square Fluctation from reference positions.
    • schrodinger.trajectory.analysis.RadiusOfGyration: A tool to calculate radius of gyration for a set of atoms.
    • schrodinger.trajectory.analysis.Ramachandran: A tool to look at Ramachandran information and plots.
    • schrodinger.trajectory.analysis.SecondaryStructure: A tool to track secondary protein structure.
    • schrodinger.trajectory.analysis.VolumeMapper: A tool to map atomic volume onto a grid.
  • schrodinger.application.desmond.simulation_block_data.Array_Prop
  • schrodinger.structutils.analyze.AslLigandSearcher: Search a Structure instance for putative ligands with an Atom Selection Language expression.
  • schrodinger.application.desmond.cmj.AslValidator
  • schrodinger.application.desmond.cms.AtomGroup
  • schrodinger.application.desmond.mdkey.AtomGroup
  • exceptions.BaseException: Common base class for all exceptions
    • exceptions.Exception: Common base class for all non-exit exceptions.
      • schrodinger.application.desmond.antlr3.exceptions.BacktrackingFailed: @brief Raised to signal failed backtrack attempt
      • schrodinger.application.canvas.similarity.CanvasSimilarityNotImplemented: For CanvasSimilarity method not yet implemented
      • schrodinger.application.desmond.systype.DetectionError
      • schrodinger.application.desmond.systype.FormatError
      • httplib.HTTPException
        • schrodinger.utils.urllib.ProxyTunnelError
      • schrodinger.application.jaguar.output.JaguarParseError
      • schrodinger.maestro.maestro.MaestroCommand: Raises an Exception and is used whenever a command fails to execute.
      • schrodinger.infra.mm.MmException: An exception class that specifically indicates the failure of an mmlibs call.
      • schrodinger.application.mopac.MopacCalculationError
      • schrodinger.structure.OptionError: A parent exception class to indicate an error in setting an option.
        • schrodinger.structure.UnsupportedOption: An exception class to indicate an attempt to set an option that is not supported.
        • schrodinger.structure.UnsupportedOptionValue: An exception class to indicate an attempt to set an option to a value that is supported.
      • schrodinger.application.desmond.cmj.ParseError
      • schrodinger.utils.urllib.PasswordRetryException
      • schrodinger.protein.assignment.PropKaException
      • schrodinger.application.bioluminate.protein.PropkaError: A custom exception for any propka failures
      • schrodinger.application.desmond.antlr3.exceptions.RecognitionException: @brief The root of the ANTLR exception hierarchy.
        • schrodinger.application.desmond.antlr3.exceptions.EarlyExitException: @brief The recognizer did not match anything for a (..)+ loop.
        • schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException: @brief A semantic predicate failed during validation.
        • schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException: @brief The next token does not match a range of expected types.
        • schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException: @brief The next token does not match a set of expected types.
          • schrodinger.application.desmond.antlr3.exceptions.MismatchedNotSetException: @brief Used for remote debugger deserialization
        • schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException: @brief A mismatched char or Token or tree node.
          • schrodinger.application.desmond.antlr3.exceptions.MissingTokenException: We were expecting a token but it's not found.
          • schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException: An extra token while parsing a TokenStream
        • schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException: @brief The next tree mode does not match the expected type.
        • schrodinger.application.desmond.antlr3.exceptions.NoViableAltException: @brief Unable to decide which alternative to choose.
      • exceptions.StandardError: Base class for all standard Python exceptions that do not represent interpreter exiting.
        • schrodinger.job.remote_command.CommandError: Used to report external commands that fail.
        • exceptions.RuntimeError: Unspecified run-time error.
          • schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException: @brief Base class for all exceptions thrown during AST rewrite construction.
            • schrodinger.application.desmond.antlr3.tree.RewriteEarlyExitException: @brief No elements within a (...)+ in a rewrite rule
            • schrodinger.application.desmond.antlr3.tree.RewriteEmptyStreamException: @brief Ref to ID or expr but no tokens in ID stream or subtrees in expr stream
      • schrodinger.application.desmond.cmj.StopRequest
      • schrodinger.application.desmond.systype.UnknownAppError
      • schrodinger.application.desmond.systype.UnknownRuleError
      • schrodinger.application.lid.ligand_interaction_diagram.UserChooseNothingException
  • schrodinger.job.queue.BaseJob: A base job class for jobs run under JobDJ.
    • schrodinger.application.desmond.cmj.JobAdapter: This adapts the `Job' class to the `que.BaseJob' class.
    • schrodinger.job.queue.JobControlJob: This class defines a job control job to be run under JobDJ.
    • schrodinger.job.queue.SubprocessJob: A job for running an external process.
    • schrodinger.job.queue.ThreadedJob: This class is for jobs that don't run under job control yet can have significant computational requirements in the python part of the JobDJ process.
  • schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer: @brief Common recognizer functionality.
    • schrodinger.application.desmond.antlr3.recognizers.Lexer: @brief Baseclass for generated lexer classes.
      • schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer
    • schrodinger.application.desmond.antlr3.recognizers.Parser: @brief Baseclass for generated parser classes.
      • schrodinger.application.desmond.antlr3.debug.DebugParser
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser
    • schrodinger.application.desmond.antlr3.tree.TreeParser: @brief Baseclass for generated tree parsers.
  • schrodinger.application.desmond.simulation_block_test.Block
  • schrodinger.application.jaguar.output.BondCharge: A class to store bond-midpoint charges calculated in ESP fitting.
  • schrodinger.application.desmond.ffiostructure.CMSReader: A class for reading structures from a CMS format file.
  • schrodinger.application.desmond.envir.CONST
  • schrodinger.analysis.enrichment.Calculator: A class to calculate enrichment terms for a screen.
  • schrodinger.application.canvas.fingerprint.CanvasFingerprint: A class to encapsulate a canvas fingerprint.
  • schrodinger.application.canvas.cluster.CanvasFingerprintCluster: A class which handles clustering of canvas fingerprints.
    • schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI: A subclass of the canvas fingerprint cluster manager which is to be used from a program with a command line interface.
    • schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI: A subclass of the canvas fingerprint clusterer which is to be used from a program with a TKInter interface.
  • schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator: A class to encapsulate canvas finger print generation.
    • schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI: A subclass of the canvas fingerprint generator which is to be used from a program with a command line interface.
    • schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI: A subclass of the canvas fingerprint generator which is to be used from a program with a TKInter interface.
  • schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity: A class which encapsulates the Canvas fingerprint similarity tools.
    • schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI: A subclass of the CanvasFingerprintSimilarity class which supports operations from the command line.
    • schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI: A subclass of the canvas fingerprint similarity manager which is to be used from a program with a TKInter interface.
  • schrodinger.structutils.interactions.CationPiInteraction: The object that stores the data for a Cation-Pi interaction
  • schrodinger.structutils.interactions.Centroid: The object that stores data about a centroid
  • schrodinger.application.desmond.mdkey.CfgAtom: This class represents the "atomic" parameters in a config file.
  • schrodinger.structutils.color.Color: Represent a color as either an integer (colormap index) or a string (color name).
  • schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin
    • schrodinger.application.bioluminate.pml_menus.AutoColorObjects
      • schrodinger.application.bioluminate.pml_menus.AutoColorCarbons
    • schrodinger.application.bioluminate.pml_menus.AutoCycleColor
      • schrodinger.application.bioluminate.pml_menus.AutoCycleCarbonColor
    • schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor
      • schrodinger.application.bioluminate.pml_menus.ColorCalphasByBFactor
    • schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum
      • schrodinger.application.bioluminate.pml_menus.ColorCalphasBySpectrum
      • schrodinger.application.bioluminate.pml_menus.ColorCarbonsBySpectrum
    • schrodinger.application.bioluminate.pml_menus.ColorBySubstructure
    • schrodinger.application.bioluminate.pml_menus.ColorChainbows
    • schrodinger.application.bioluminate.pml_menus.ColorChains
      • schrodinger.application.bioluminate.pml_menus.ColorChainsByCalpha
      • schrodinger.application.bioluminate.pml_menus.ColorChainsByCarbon
    • schrodinger.application.bioluminate.pml_menus.CustomColor
      • schrodinger.application.bioluminate.pml_menus.ColorCarbons
      • schrodinger.application.bioluminate.pml_menus.ColorHydrogens
      • schrodinger.application.bioluminate.pml_menus.ColorObject
    • unreachable.CustomRecentColor
      • schrodinger.application.bioluminate.pml_menus.ColorRecentCarbons
      • schrodinger.application.bioluminate.pml_menus.ColorRecentHydrogens
      • schrodinger.application.bioluminate.pml_menus.ColorRecentObjects
  • schrodinger.application.glide.xp6classes.Complex: Class to generate and store experimental and newXP information for a single protein-ligand complex
    • schrodinger.application.glide.xp6classes.NewxpJobdata
  • schrodinger.application.desmond.cms.Constraint
  • _abcoll.Container
    • _abcoll.Mapping
      • _abcoll.MutableMapping
        • collections.OrderedDict: Dictionary that remembers insertion order
          • schrodinger.application.bioluminate.protein.OrderedResidueDict: Creates an ordered dictionary for residues in a structure
    • _abcoll.Sequence: All the operations on a read-only sequence.
      • _abcoll.MutableSequence
        • UserList.UserList
          • schrodinger.structutils.sort.DsuList: A class to sort a list with special behaviors.
  • schrodinger.application.desmond.util.Counter: This class was originally designed for the convenience of gridding widgets.
  • schrodinger.infra.util.CreateWhenNeeded: This class can be used like property() (i.e., it is a descriptor; see section 3.3.2.2 in the python reference).
  • schrodinger.application.qsite.input.Cut: A class to handle representation and printing of general qm region cuts.
  • schrodinger.application.desmond.config.DEFAULT_SETTING
  • schrodinger.application.desmond.antlr3.dfa.DFA: @brief A DFA implemented as a set of transition tables.
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1
    • schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24
    • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25
  • schrodinger.application.desmond.antlr3.dottreegen.DOTTreeGenerator: A utility class to generate DOT diagrams (graphviz) from arbitrary trees.
  • schrodinger.application.desmond.antlr3.debug.DebugEventListener: All debugging events that a recognizer can trigger.
    • schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener: A blank listener that does nothing; useful for real classes so they don't have to have lots of blank methods and are less sensitive to updates to debug interface.
    • schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy: A proxy debug event listener that forwards events over a socket to a debugger (or any other listener) using a simple text-based protocol; one event per line.
    • schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener: A listener that simply records text representations of the events.
      • schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener: A listener that records events as strings in an array.
  • schrodinger.application.desmond.fepana.DeltaEnergy
  • schrodinger.application.jaguar.output.Dipole: A class for storing dipole information.
  • schrodinger.application.desmond.cmj.Engine
  • schrodinger.application.glide.ensemble_selection.Ensemble: Objects of this class are basically dumb "structs" that hold the basic attributes of a specific ensemble.
  • schrodinger.application.glide.xp6classes.EnsembleLigand: Store information about test-set ligands, as derived from Glide ensemble docking.
  • schrodinger.application.glide.ensemble_selection.EnsembleSelection: Objects of this class select the "best"(*) ensembles of a specified size when given as input the results from an exhaustive cross-docking calculation on a set of N complexes (i.e., the NxN matrix of GlideScores).
  • schrodinger.application.desmond.maestro.Entry: A class for representing an entry in the Project Table.
  • schrodinger.project.EntryGroup: A class which represents an entry group in the project table.
  • schrodinger.application.desmond.maestro.EntryGroup: A class for representing an entry group in the Project Table
  • schrodinger.application.desmond.util.EntryRestrictor: Similar to EntryFieldRestrictor, but for the 'Entry' widget instead of the 'EntryField' widget.
  • schrodinger.project.EntrySurface: A class for accessing the surfaces associated with a given entry.
  • schrodinger.application.desmond.enhsamp.Env
  • schrodinger.infra.mmerr.ErrorHandler: A class for managing mmerr handlers.
  • schrodinger.application.bioluminate.pml_menus.FakeMaestro
  • schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro
  • schrodinger.application.desmond.mdkey.FepSchedule
  • schrodinger.structure.FormatReader: This is a base class for all file format readers.
    • schrodinger.structure.MaestroReader: A class for reading structures from a Maestro (M2io) format file.
      • schrodinger.structure.MaestroReaderWithPositions: A class for rapid random access to the structures in a Maestro file.
    • schrodinger.structure.Mol2Reader: A class for reading structures from a mol2 format file.
    • schrodinger.structure.PDBReader: A class for reading structures from a PDB format file.
    • schrodinger.structure.SDReader: A class for reading structures from a SD format file.
  • schrodinger.trajectory.atomselection.FrameAslSelection: A class for selecting atoms from frames in a given simulation using ASL.
  • schrodinger.trajectory.atomselection.FrameIndexSelection: A class that defines a static set of indices to be selected from all frames.
  • schrodinger.trajectory.atomselection.FrameSliceSelection: A class for efficiently selecting a range of atoms.
  • schrodinger.application.bioluminate.antibody_utils.FrameworkTemplate
  • schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate
  • schrodinger.application.desmond.fepana.FreeEnergyContrib
  • schrodinger.application.jaguar.output.FukuiIndices: A class to store Atomic Fukui indices.
  • schrodinger.application.jaguar.input.GenOptions: A class to convert keyword value pairs defined in a single string into a data structure, and allow them to be converted back into a string.
  • schrodinger.trajectory.analysis.Grid3D: A class for representing a function of 3D Cartesian coordinates discretize onto a grid.
  • schrodinger.graphics3d.common.Group: Class to group a bunch of primitives and draw them out.
  • schrodinger.application.desmond.multisimstartup.Help
  • schrodinger.application.desmond.config._FepSchedule.Helper
  • schrodinger.job.jobcontrol.Host: A class to encapsulate host info from the schrodinger.hosts file.
  • schrodinger.job.hunt_cache.HuntCache: A HuntCache object represents a particular "hunt cache" a file that stores hunt results for re-use.
  • schrodinger.application.qsite.input.HydrogenCap: A class to handle representation and printing of hydrogen caps for the qm region.
  • schrodinger.application.phase.hypothesis.Hypothesis
  • schrodinger.utils.timers.IncrementalTimer: Track absolute total and incremental wall and CPU time and, optionally, times per item processed, possibly for several types of item.
  • schrodinger.application.desmond.util.InfAutofill
  • schrodinger.infra.mminit.Initializer: A class to handle initialization and termination of needed mmlibs.
    • schrodinger.job.jobcontrol._JobInitializer: A class to handle class initialization and termination.
  • schrodinger.application.desmond.antlr3.streams.IntStream: @brief Base interface for streams of integer values.
    • schrodinger.application.desmond.antlr3.streams.CharStream: @brief A source of characters for an ANTLR lexer.
      • schrodinger.application.desmond.antlr3.streams.ANTLRStringStream: @brief CharStream that pull data from a unicode string.
        • schrodinger.application.desmond.antlr3.streams.ANTLRFileStream: @brief CharStream that opens a file to read the data.
        • schrodinger.application.desmond.antlr3.streams.ANTLRInputStream: @brief CharStream that reads data from a file-like object.
    • schrodinger.application.desmond.antlr3.streams.TokenStream: @brief A stream of tokens accessing tokens from a TokenSource
      • schrodinger.application.desmond.antlr3.streams.CommonTokenStream: @brief The most common stream of tokens
        • schrodinger.application.desmond.antlr3.streams.TokenRewriteStream: @brief CommonTokenStream that can be modified.
      • schrodinger.application.desmond.antlr3.debug.DebugTokenStream
    • schrodinger.application.desmond.antlr3.tree.TreeNodeStream: @brief A stream of tree nodes
      • schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream: @brief A buffered stream of tree nodes.
  • schrodinger.application.bioluminate.pml_menus.InterfaceMixin: Determine the Protein-Protein interface atoms
    • schrodinger.application.bioluminate.pml_menus.GenerateInterfaceSelection
    • schrodinger.application.bioluminate.pml_menus.InterfacePreset
  • _abcoll.Iterable
    • _abcoll.Mapping
      • _abcoll.MutableMapping
        • collections.OrderedDict: Dictionary that remembers insertion order
          • schrodinger.application.bioluminate.protein.OrderedResidueDict: Creates an ordered dictionary for residues in a structure
    • _abcoll.Sequence: All the operations on a read-only sequence.
      • _abcoll.MutableSequence
        • UserList.UserList
          • schrodinger.structutils.sort.DsuList: A class to sort a list with special behaviors.
  • schrodinger.application.jaguar.output.JaguarAtomicResults: A class for holding atomic level properties.
  • schrodinger.application.jaguar.input.JaguarInput: A class for specifying Jaguar input.
  • schrodinger.application.jaguar.output.JaguarOptions: A class for keeping track of specific calculation options.
  • schrodinger.application.jaguar.output.JaguarOutput: A class for accessing Jaguar output properties.
    • schrodinger.application.qsite.output.QSiteOutput: A class to hold output information from a QSite run.
  • schrodinger.application.jaguar.output.JaguarResults: A class for holding results for a specific geometry.
    • schrodinger.application.qsite.output.QSiteResults: A class for holding results for a specific geometry.
  • schrodinger.job.jobcontrol.Job: A class to access a specific record in the job database.
  • schrodinger.application.desmond.cmj.Job
    • schrodinger.application.desmond.stage.AnalysisJob
      • schrodinger.application.desmond.stage.SeaJob
      • schrodinger.application.desmond.stage.TimeSeriesAnalysisJob
    • schrodinger.application.desmond.stage.DesmondJob
      • schrodinger.application.desmond.stage.FepJob
      • schrodinger.application.desmond.stage.FepanaJob
    • schrodinger.application.desmond.stage.MetadynamicsAnalysisJob
    • schrodinger.application.desmond.stage.WaterMapAnaJob
  • schrodinger.job.queue.JobDJ: Class for running commands/jobs in parallel under jobcontrol.
  • schrodinger.application.desmond.cmj.JobErrorHandler
  • schrodinger.ui.qt.appframework.JobInputParams: A class to store the state of the JobInputFrame, and to control behavior needed to create access to structure files.
  • schrodinger.ui.appframework.JobInputParams: A class to store the state of the JobInputFrame, and to control behavior needed to create access to structure files.
    • schrodinger.ui.appframework.MultiInputParams: A class to hold the state of the MultiInputFrame and set up files needed by backend calculations.
  • schrodinger.application.desmond.cmj.JobOutput
    • schrodinger.application.desmond.cmj.JobInput
  • schrodinger.application.desmond.cmj.JobStatus
  • schrodinger.application.desmond.mdkey.Key
  • schrodinger.infra.licensing.License
    • schrodinger.infra.licensing.LicensePtr
  • schrodinger.application.bioluminate.license.License: Class to allow easy licensing of BioLuminate scripts
  • schrodinger.structutils.analyze.Ligand: A putative AslLigandSearcher ligand structure with read-only data and convenience methods.
  • schrodinger.application.bioluminate.pml_menus.LigandActionMixin: Class that contains a method to restrict the asl to Ligands only
    • schrodinger.application.bioluminate.pml_menus.ExcludeOrganicFromSelection
    • schrodinger.application.bioluminate.pml_menus.GenerateLigandSelection
    • schrodinger.application.bioluminate.pml_menus.PresetAction: Base class for Preset Actions
      • schrodinger.application.bioluminate.pml_menus.AntibodyPreset
      • schrodinger.application.bioluminate.pml_menus.BAndSPreset
      • schrodinger.application.bioluminate.pml_menus.BFactorPreset
      • schrodinger.application.bioluminate.pml_menus.DefaultPreset
      • schrodinger.application.bioluminate.pml_menus.InterfacePreset
      • schrodinger.application.bioluminate.pml_menus.LigandPreset
      • schrodinger.application.bioluminate.pml_menus.PrettyPubPreset: Show the object as nice-looking cartoon ribbons
      • schrodinger.application.bioluminate.pml_menus.SimplePreset
      • schrodinger.application.bioluminate.pml_menus.TechnicalPreset
    • schrodinger.application.bioluminate.pml_menus.RestrictToOrganic
    • schrodinger.application.bioluminate.pml_menus.ShowLigandLines
    • schrodinger.application.bioluminate.pml_menus.ShowLigandSpheres
    • schrodinger.application.bioluminate.pml_menus.ShowLigandTubes
  • schrodinger.job.queue.LinkedList: A doubly linked list, providing constant time addition, size, and truth checks.
    • schrodinger.job.queue.RunningJobs: A LinkedList subclass that tracks running jobs and keeps a tally of jobs running on each machine.
  • schrodinger.job.queue.LinkedListNode: A node for the LinkedList class, holding a value, and a reference to the previous and next node in the list.
  • schrodinger.structure.MaestroTextReader: A class for reading structures from a Maestro format file.
  • schrodinger.application.desmond.measurement.Measurement: Basic method for uncertainty propagation: Say we have a few measurements: x1, x2, x3, ..., and they each has a uncertainty: d1, d2, d3, ..., respectively.
  • schrodinger.application.desmond.enhsamp.Meta
  • schrodinger.structutils.minimize.Minimizer: A class to provide force field energy and minimization.
  • schrodinger.infra.mmobject.MmObject: An abstraction of the bookkeeping needed to create a garbage collected MM object.
    • schrodinger.infra.mmbitset.Bitset: This class represents a bitset, with each element either 1 or 0.
    • schrodinger.application.jaguar.mmjag.MmJag: A reference counting class for dealing with mmjag handles.
    • schrodinger.project.Project: Class to handle Maestro Projects.
    • schrodinger.infra.table.Table: Class to handle mmtables.
    • schrodinger.infra.mmlist.mmlist: Wrap an anderlying mmlist "instance" and provides access to its members through the python sequence syntax.
  • schrodinger.utils.moduleproxy.ModuleProxy: A class to use as a placeholder for a non-essential module, raising an exception when something tries to use it.
  • schrodinger.application.moldescriptors.MolecularDescriptorsOptions: A class to provide various options that can be passed to calculate molecular descriptors.
  • schrodinger.application.mopac.MopacCalculation: A class for running MOPAC calculations.
  • schrodinger.application.mopac.MopacResults: A class to store MOPAC results.
  • schrodinger.application.desmond.enhsamp.Node
    • schrodinger.application.desmond.enhsamp.Bind
    • schrodinger.application.desmond.enhsamp.FcnCall
    • schrodinger.application.desmond.enhsamp.If
    • schrodinger.application.desmond.enhsamp.Iter
    • schrodinger.application.desmond.enhsamp.Let
    • schrodinger.application.desmond.enhsamp.Lit
    • schrodinger.application.desmond.enhsamp.Series
    • schrodinger.application.desmond.enhsamp.String
    • schrodinger.application.desmond.enhsamp.Var
  • schrodinger.application.jaguar.output.NormalMode: A class for storing normal mode results.
  • schrodinger.application.jaguar.output.Orbital: A class for storing orbital information.
  • schrodinger.structure.PDBWriter: A class for writing PDB-formatted files.
  • schrodinger.structutils.interactions.PiPiInteraction: The object that stores the data for a Pi-Pi interaction
  • schrodinger.application.desmond.picklejar.Picklable
    • schrodinger.application.desmond.stage.FepJob
    • schrodinger.application.desmond.stage.FepanaJob
    • schrodinger.application.desmond.cmj.StageBase
      • schrodinger.application.desmond.stage.Analysis
      • schrodinger.application.desmond.stage.AssignForcefield
      • schrodinger.application.desmond.stage.BuildGeometry
      • schrodinger.application.desmond.stage.Concluder: This stage does not create any jobs for the 'cmj.QUEUE'.
      • schrodinger.application.desmond.stage.Extern
      • schrodinger.application.desmond.stage.FepAnalysis
      • schrodinger.application.desmond.stage.McproStageBase
        • schrodinger.application.desmond.stage.McproSimulate
        • schrodinger.application.desmond.stage.McproSystemBuilder
      • schrodinger.application.desmond.stage.Multisim: Unimplemented stage.
      • schrodinger.application.desmond.stage.Primer
      • schrodinger.application.desmond.stage.Simulate
        • schrodinger.application.desmond.stage.FepVrun
        • schrodinger.application.desmond.stage.Minimize
        • schrodinger.application.desmond.stage.ReplicaExchange
          • schrodinger.application.desmond.stage.LambdaHopping
        • schrodinger.application.desmond.stage.Vrun
      • schrodinger.application.desmond.stage.SolvatePocket
      • schrodinger.application.desmond.stage.Stop
      • schrodinger.application.desmond.stage.SystemBuilder
      • schrodinger.application.desmond.stage.Task
      • schrodinger.application.desmond.stage.Trajectory
      • schrodinger.application.desmond.stage.Trim
      • schrodinger.application.desmond.stage.WaterMap
      • schrodinger.application.desmond.stage.WaterMapCluster
      • schrodinger.application.desmond.stage.WaterMapPostAnalysis
  • schrodinger.application.desmond.picklejar.PickleJar
  • schrodinger.application.desmond.picklejar.PickleState
  • schrodinger.analysis.enrichment.Plotter: A class to plot multiple series of Calculator data.
  • schrodinger.utils.preferences.Preferences: A class that allows Pythonic access to the mmpref library.
  • schrodinger.graphics3d.common.Primitive: All 3D objects derive from this class.
    • schrodinger.graphics3d.arrow.ArrowCore: Base class for drawing a 3D arrow
      • schrodinger.graphics3d.arrow.Arrow: Class for drawing a 3D arrow in OpenGL.
      • schrodinger.graphics3d.arrow.MaestroArrow: Class for creating a 3D arrow in Maestro
    • schrodinger.graphics3d.box.Box: Class to draw a 3D box in OpenGL.
    • schrodinger.graphics3d.lines.Lines: Class to draw a set of lines in OpenGL.
    • schrodinger.graphics3d.polygon.Polygon: Class to draw a flat polygon in OpenGL.
    • schrodinger.graphics3d.polyhedron.Polyhedron: Class to draw a 3D polyhedron with OpenGL using the current context in whatever is the current drawable (which could be Maestro).
      • schrodinger.graphics3d.polyhedron.PolyhedronCore
        • schrodinger.graphics3d.polyhedron.Cube: Class to draw a 3D cube in Maestro's Workspace.
        • schrodinger.graphics3d.polyhedron.Dodecahedron: Class to draw a 3D dodecahedron in Maestro's Workspace.
        • schrodinger.graphics3d.polyhedron.Icosahedron: Class to draw a 3D icosahedron in Maestro's Workspace.
        • schrodinger.graphics3d.polyhedron.Octahedron: Class to draw a 3D octahedron in Maestro's Workspace.
        • schrodinger.graphics3d.polyhedron.Tetrahedron: Class to draw a 3D tetrahedron in Maestro's Workspace.
    • schrodinger.graphics3d.quadrilateral.Quadrilateral: Class to draw a 3D quadrilateral in OpenGL.
    • schrodinger.graphics3d.sphere.SphereCore: Base class for Sphere and MaestroSphere classes.
      • schrodinger.graphics3d.sphere.MaestroSphere: Class to create a 3D sphere in Maestro.
      • schrodinger.graphics3d.sphere.Sphere: Class to draw a 3D sphere in OpenGL.
  • multiprocessing.process.Process: Process objects represent activity that is run in a separate process
    • schrodinger.trajectory.rmsd2d.RMSDMultiprocessing
  • schrodinger.project.ProjectRow: ProjectRow allows access to the structure and properties of an entry in the project.
  • schrodinger.application.bioluminate.protein.PropertyCalculator: Class for calculating properties of proteins and protein residues.
  • schrodinger.structure.PropertyName: The PropertyName class can be used to display the "user-readable" version of an entry or atom property to the user.
  • schrodinger.application.desmond.cms.Pseudo
  • schrodinger.application.qsite.input.QMRegion: A class to provide access to a &qmregion specification and the ability to create one on the fly.
  • schrodinger.application.qsite.input.QSiteInput
  • schrodinger.application.desmond.cmj.Queue
  • schrodinger.application.desmond.antlr3.recognizers.RecognizerSharedState: The set of fields needed by an abstract recognizer to recognize input and recover from errors etc...
  • schrodinger.application.bioluminate.pml_menus.RegionInfo
  • schrodinger.application.desmond.stage.Reporter
  • schrodinger.job.queue.RequirementsJob: This is a base class that indicates a job has special requirements (e.g.
    • schrodinger.job.queue.LocalhostJob: This class should be used as a mixin on a job type that requires jobs to be run on localhost.
      • schrodinger.job.queue.SubprocessJob: A job for running an external process.
  • schrodinger.application.desmond.cms.Restrain
  • schrodinger.application.desmond.cmj.RetryTimer
  • schrodinger.application.desmond.antlr3.streams.RewriteOperation: @brief Internal helper class.
    • schrodinger.application.desmond.antlr3.streams.InsertBeforeOp: @brief Internal helper class.
    • schrodinger.application.desmond.antlr3.streams.ReplaceOp: @brief Internal helper class.
      • schrodinger.application.desmond.antlr3.streams.DeleteOp: @brief Internal helper class.
  • schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream: @brief Internal helper class.
    • schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream: Queues up nodes matched on left side of -> in a tree parser.
    • schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream: @brief Internal helper class.
    • schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream: @brief Internal helper class.
  • schrodinger.application.bioluminate.pml_menus.RockData: Stores information about the current workspace rocking state
  • schrodinger.protein.rotamers.Rotamers: Manages a rotamer library for a given residue type.
  • schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope: Rules can return start/stop info as well as possible trees and templates.
    • schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope: Rules that return more than a single value must return an object containing all the values.
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.atom_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.bind_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.block_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.comp_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_meta_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_output_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expComp_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.exprOrBind_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expr_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.factor_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.fcnCall_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.header_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.if__return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.iter_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.meta_term_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.output_term_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.prog_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.series_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.signedExpComp_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.static_return
      • schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.varWithType_return
    • schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope: This is identical to the ParserRuleReturnScope except that the start property is a tree nodes not Token object when you are parsing trees.
  • schrodinger.application.jaguar.scan.Scan: A class for storing information about geometry scan variables.
  • schrodinger.application.jaguar.output.ScfIteration: A simple storage class for storing info on an SCF iteration.
  • schrodinger.utils.sea.Sea: This is the base class the 'Atom', 'List', and 'Map' classes.
    • schrodinger.utils.sea.Atom: This class represents the "atomic" parameters in a config file.
    • schrodinger.utils.sea.List: This class represents the "list" parameters in a config file.
    • schrodinger.utils.sea.Map: This class represents the "map" parameters in a config file.
  • schrodinger.antibody_db_manage_gui.SearchType: Information about and widgets for each set of structures that are to be added to the Database
  • schrodinger.application.desmond.cms.Site
  • _abcoll.Sized
    • _abcoll.Mapping
      • _abcoll.MutableMapping
        • collections.OrderedDict: Dictionary that remembers insertion order
          • schrodinger.application.bioluminate.protein.OrderedResidueDict: Creates an ordered dictionary for residues in a structure
    • _abcoll.Sequence: All the operations on a read-only sequence.
      • _abcoll.MutableSequence
        • UserList.UserList
          • schrodinger.structutils.sort.DsuList: A class to sort a list with special behaviors.
  • schrodinger.application.ska.SkaData: Data structure for named backend return values...
  • schrodinger.application.bioluminate.sliderchart.SlidableLine: A line on a matplotlib plot that can be grabbed and moved by the user
    • schrodinger.application.bioluminate.sliderchart.SlidableHLine: A horizontal line on a matplotlib plot that can be grabbed and moved by the user
    • schrodinger.application.bioluminate.sliderchart.SlidableVLine: A vertical line on a matplotlib plot that can be grabbed and moved by the user
  • schrodinger.structure.SmilesCsvReader: A class for reading structures from a SMILES CSV formatted file.
  • schrodinger.structure.SmilesReader: A class for reading structures from a SMILES formatted file.
  • schrodinger.structure.SmilesStructure: SMILES representation of a Structure that is returned by SmilesReader and SmilesCsvReader.
  • schrodinger.ui.appframework.StartDialogParams: A collection of parameter values from the StartDialog class.
  • schrodinger.ui.qt.appframework.StartDialogParams: A collection of parameter values from the StartDialog class.
  • schrodinger.application.desmond.multisimstartup.Startup
  • schrodinger.application.bioluminate.propfilter.StringDatabaseCriterion: Holds a criterion for a string property and determines whether a database object or structure meets that criterion
    • schrodinger.application.bioluminate.propfilter.BooleanDatabaseCriterion
    • schrodinger.application.bioluminate.propfilter.NumericalDatabaseCriterion
  • schrodinger.structutils.structalign.StructAlign: This is the class used to perform the structural alignment.
  • schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator: A class which generates Structural Interaction Fingerprints.
  • schrodinger.structure.Structure: A general chemical structure object, which may contain multiple molecules.
    • schrodinger.application.desmond.cms.Cms
    • schrodinger.trajectory.cmsstructure.CmsStructure: CmsStructure represents a complete description of Desmond model system, which includes one full ct and several component cts.
    • schrodinger.application.desmond.ffiostructure.FFIOStructure: Class to create python interface to force field data.
    • schrodinger.structure.TextualStructure: A sub-class of Structure for use when reading from a Maestro format file and only the structure-level properties are needed.
  • schrodinger.application.desmond.stage.FepAnalysis.Structure
  • schrodinger.structure.StructureReader: A class to read structures from files of various types.
  • schrodinger.structure.StructureWriter: A class for efficient writing of multiple structures to a single structure file.
  • schrodinger.trajectory.analysis.Superimposer
  • schrodinger.application.desmond.enhanced_sampling.FcnTypes.Syntax
    • schrodinger.application.desmond.enhanced_sampling.FcnTypes.ArraySyntax
    • schrodinger.application.desmond.enhanced_sampling.FcnTypes.BinaryThreadSyntax
    • schrodinger.application.desmond.enhanced_sampling.FcnTypes.MetaSyntax
    • schrodinger.application.desmond.enhanced_sampling.FcnTypes.RMSDSyntax
    • schrodinger.application.desmond.enhanced_sampling.FcnTypes.SimpleSyntax
    • schrodinger.application.desmond.enhanced_sampling.FcnTypes.ThreadSyntax
  • schrodinger.application.desmond.systype.SysType
  • schrodinger.application.desmond.simulation_block_test.Test
    • schrodinger.application.desmond.simulation_block_test.BoxSize
    • schrodinger.application.desmond.simulation_block_test.E_f
    • schrodinger.application.desmond.simulation_block_test.E_k
    • schrodinger.application.desmond.simulation_block_test.E_x
    • schrodinger.application.desmond.simulation_block_test.Energy
    • schrodinger.application.desmond.simulation_block_test.Job_Details
    • schrodinger.application.desmond.simulation_block_test.PotentialEnergy
    • schrodinger.application.desmond.simulation_block_test.Pressure
    • schrodinger.application.desmond.simulation_block_test.T_0
    • schrodinger.application.desmond.simulation_block_test.Temperature
    • schrodinger.application.desmond.simulation_block_test.V
  • schrodinger.application.desmond.util.TestSuite: A small and tight class designed for unit tests.
  • schrodinger.application.jaguar.output.TextParser: A parser to create a JaguarOutput object from a Jaguar output file.
    • schrodinger.application.qsite.output.QSiteTextParser: A subclass of the Jaguar output text parser that adds QSite specific parsing.
  • schrodinger.application.jaguar.output.ThermoCollection: A class to store a full set of calculated thermodynamic properties at a given temperature.
  • schrodinger.application.jaguar.output.ThermoProp: A class to store the components of calculated thermodynamic properties.
  • schrodinger.application.desmond.cmj.Job.Time
  • schrodinger.application.desmond.antlr3.tokens.Token: @brief Abstract token baseclass.
    • schrodinger.application.desmond.antlr3.tokens.ClassicToken: @brief Alternative token implementation.
    • schrodinger.application.desmond.antlr3.tokens.CommonToken: @brief Basic token implementation.
  • schrodinger.application.desmond.antlr3.recognizers.TokenSource: @brief Abstract baseclass for token producers.
    • schrodinger.application.desmond.antlr3.recognizers.Lexer: @brief Baseclass for generated lexer classes.
      • schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer
  • schrodinger.application.desmond.antlr3.tree.Tree: @brief Abstract baseclass for tree nodes.
    • schrodinger.application.desmond.antlr3.tree.BaseTree: @brief A generic tree implementation with no payload.
      • schrodinger.application.desmond.antlr3.tree.CommonTree: @brief A tree node that is wrapper for a Token object.
        • schrodinger.application.desmond.antlr3.tree.CommonErrorNode: A node representing erroneous token range in token stream
        • schrodinger.application.desmond.antlr3.treewizard.TreePattern: When using %label:TOKENNAME in a tree for parse(), we must track the label.
          • schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern
  • schrodinger.application.desmond.antlr3.tree.TreeAdaptor: @brief Abstract baseclass for tree adaptors.
    • schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor: @brief A TreeAdaptor that works with any Tree implementation.
      • schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor: @brief A TreeAdaptor that works with any Tree implementation.
        • schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor: This adaptor creates TreePattern objects for use during scan()
    • schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor: A TreeAdaptor proxy that fires debugging events to a DebugEventListener delegate and uses the TreeAdaptor delegate to do the actual work.
  • schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer
  • schrodinger.application.desmond.antlr3.treewizard.TreePatternParser
  • schrodinger.application.desmond.antlr3.tree.TreeVisitor: Do a depth first walk of a tree, applying pre() and post() actions we go.
  • schrodinger.application.desmond.antlr3.treewizard.TreeWizard: Build and navigate trees with this object.
  • schrodinger.application.desmond.systype.TyperBase
    • schrodinger.application.desmond.systype.DesmondTyper
    • schrodinger.application.desmond.systype.McproTyper
    • schrodinger.application.desmond.systype.WatermapTyper
  • schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog
  • schrodinger.application.lid.lid_savedialog_ui.Ui_Dialog
  • schrodinger.application.bioluminate.propfilter_ui.Ui_Form
  • schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form
  • schrodinger.application.lid.ligand_interaction_diagram_ui.Ui_Form
  • schrodinger.ui.ligfilter_ui.Ui_Form
  • schrodinger.application.desmond.cms.Vdw: A class for handling VDW parameters.
  • schrodinger.ui.widgettable.WidgetTable: The table class with scroll bars
  • schrodinger.application.desmond.maestro.Workspace: A class for representing the Workspace.
  • schrodinger.structure._AtomBondContainer: The class to provide access to _StructureBond instances for each bond of an atom.
  • schrodinger.application.desmond.gui._AtomGroup: Represents the data of the atom group table? Of the Misc tab of the Advanced Options dialog
  • schrodinger.structure._AtomIterator: Iterates over each _StructureAtom in a _Molecule, _Chain, _Residue or _Ring.
  • schrodinger.trajectory.atomselection._AtomSelection: A general class for ASL expression support.
  • schrodinger.application.jaguar.output._Attribute: A small utility class to automate and regularize handling of attributes.
  • schrodinger.job.jobcontrol._Backend: An interface to mmjobbe.
    • schrodinger.application.desmond.meta._Backend
  • schrodinger.structure._BaseWriter: This class provides a common implementation for structure writers.
    • schrodinger.structure.MaestroWriter: A class for more efficient appending of a large number of structures to a single maestro structure file.
    • schrodinger.structure.Mol2Writer: Mol2 support for the StructureWriter class.
    • schrodinger.structure.SDWriter: A class for more efficient appending of a large number of structures to a single SD structure file.
    • schrodinger.structure.SmilesCsvWriter: A class for more efficient writing of a large number of structures to a single SMILES CSV file.
    • schrodinger.structure.SmilesWriter: A class for more efficient writing of a large number of structures to a single SMILES file.
  • schrodinger.application.desmond.mdkey._Bool
  • schrodinger.structure._Chain: A class used to return chain information when iterating over chains in a Structure object.
  • schrodinger.ui.widgettable._Column: Base class for a column
    • schrodinger.ui.widgettable.ButtonColumn: Class defining a column of Buttons
    • schrodinger.ui.widgettable.CanvasColumn: Class defining a column of Canvas objects
    • schrodinger.ui.widgettable.CheckbuttonColumn: Class defining a column of checkbuttons
    • schrodinger.ui.widgettable.EntryFieldColumn: Class defining a column of EntryField cells
    • schrodinger.ui.widgettable.LabelColumn: Class defining a column of Labels
    • schrodinger.ui.widgettable.OptionMenuColumn: Class defining a column of OptionMenuCells.
    • schrodinger.ui.widgettable.RadiobuttonColumn: Class defining a column of Radiobuttons
  • schrodinger.structutils.measure._DistanceCell
  • schrodinger.application.desmond.ffiostructure._Element
    • schrodinger.application.desmond.ffiostructure._FEPIOElement: hash(x)
    • schrodinger.application.desmond.ffiostructure._FFIOElement: hash(x)
  • schrodinger.application.desmond.mdkey._Evalor
  • schrodinger.utils.sea._Evalor: This is the evaluator class for checking validity of parameters.
  • schrodinger.application.desmond.ffiostructure._FEPIO: A class to make access of fepio block pythonic.
  • schrodinger.application.desmond.ffiostructure._FEPIOSubBlock: A class to make access of fepio sub-block properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FEPIOAngleMap: hash(x)
    • schrodinger.application.desmond.ffiostructure._FEPIOAtomMap: hash(x)
    • schrodinger.application.desmond.ffiostructure._FEPIOBondMap: hash(x)
    • schrodinger.application.desmond.ffiostructure._FEPIODihedMap: hash(x)
    • schrodinger.application.desmond.ffiostructure._FEPIOExclMap: hash(x)
    • schrodinger.application.desmond.ffiostructure._FEPIOPairMap: hash(x)
  • schrodinger.application.desmond.ffiostructure._FEPIOSubBlockContainer
    • schrodinger.application.desmond.ffiostructure._FEPIOAngleMapContainer
    • schrodinger.application.desmond.ffiostructure._FEPIOAtomMapContainer
    • schrodinger.application.desmond.ffiostructure._FEPIOBondMapContainer
    • schrodinger.application.desmond.ffiostructure._FEPIODihedMapContainer
    • schrodinger.application.desmond.ffiostructure._FEPIOExclMapContainer
    • schrodinger.application.desmond.ffiostructure._FEPIOPairMapContainer
  • schrodinger.trajectory.ffstructure._FFAngle: A class to hold force field parameters for an angle.
  • schrodinger.trajectory.ffstructure._FFBond: A class to hold force field parameters for a bond.
  • schrodinger.trajectory.ffstructure._FFConstraint: A class to hold force field parameters for a constraint.
  • schrodinger.trajectory.ffstructure._FFDihedral: A class to hold force field parameters for a dihedral.
  • schrodinger.trajectory.ffstructure._FFExclusion: A class to hold force field parameters for an exclusion pair.
  • schrodinger.application.desmond.ffiostructure._FFIO: A class to make access of ffio block pythonic.
  • schrodinger.application.desmond.ffiostructure._FFIOSubBlock: A class to make access of ffio sub-block properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOAngle: A class to make access of mmffio angle properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOAngleFBHW: A class to make access of mmffio angle flat bottom properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOBond: A class to make access of mmffio bond properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOConstraint: A class to make access of mmffio constraint properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIODihedral: A class to make access of mmffio dihedral properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOExclusion: A class to make access of mmffio exclusion properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOImproperFBHW: A class to make access of mmffio improper flat bottom properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOPair: A class to make access of mmffio pair properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOPosFBHW: A class to make access of mmffio position flat bottom properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOPseudo: A class to make access of mmffio pseudo properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIORestraint: A class to make access of mmffio restraint properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOSite: A class to make access of mmffio site properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOStretchFBHW: A class to make access of mmffio stretch flat bottom properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOVdwtype: A class to make access of mmffio vdwtype properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOVdwtypescombined: A class to make access of mmffio vdwtype properties more pythonic.
    • schrodinger.application.desmond.ffiostructure._FFIOVirtual: A class to make access of mmffio virtual properties more pythonic.
  • schrodinger.application.desmond.ffiostructure._FFIOSubBlockContainer
    • schrodinger.application.desmond.ffiostructure._FFIOAngleContainer
    • schrodinger.application.desmond.ffiostructure._FFIOAngleFBHWContainer
    • schrodinger.application.desmond.ffiostructure._FFIOBondContainer
    • schrodinger.application.desmond.ffiostructure._FFIOConstraintContainer
    • schrodinger.application.desmond.ffiostructure._FFIODihedralContainer
    • schrodinger.application.desmond.ffiostructure._FFIOExclusionContainer
    • schrodinger.application.desmond.ffiostructure._FFIOImproperFBHWContainer
    • schrodinger.application.desmond.ffiostructure._FFIOPairContainer
    • schrodinger.application.desmond.ffiostructure._FFIOPosFBHWContainer
    • schrodinger.application.desmond.ffiostructure._FFIOPseudoContainer
    • schrodinger.application.desmond.ffiostructure._FFIORestraintContainer
    • schrodinger.application.desmond.ffiostructure._FFIOSiteContainer
    • schrodinger.application.desmond.ffiostructure._FFIOStretchFBHWContainer
    • schrodinger.application.desmond.ffiostructure._FFIOVdwtypeContainer
    • schrodinger.application.desmond.ffiostructure._FFIOVdwtypescombinedContainer
    • schrodinger.application.desmond.ffiostructure._FFIOVirtualContainer
  • schrodinger.trajectory.ffstructure._FFPair: A class to hold force field parameters for a pair.
  • schrodinger.trajectory.ffstructure._FFPseudo: A class to hold force field parameters for a pseudo atom.
  • schrodinger.trajectory.ffstructure._FFRestraint: A class to hold force field parameters for a restraint.
  • schrodinger.trajectory.ffstructure._FFSite: A class to hold force field parameters for a site.
  • schrodinger.trajectory.ffstructure._FFVdwtype: A class to hold force field parameters for a Van der Waals type.
  • schrodinger.trajectory.ffstructure._FFVirtual: A class to hold force field parameters for a virtual site.
  • schrodinger.application.desmond.config._FepSchedule
  • schrodinger.application.desmond.icon._Global: A class to hold global objects so the use of module-level objects can be avoided.
  • schrodinger.job.jobcontrol._JobManager
  • schrodinger.job.jobcontrol._JobResourceHolder: A helper class to deal with mmlib resource de-allocation.
  • schrodinger.application.desmond.antlr3.main._Main
  • schrodinger.application.desmond.gui._MdcBase: The Advanced options dialogs and their tab widgets subclass this class.
    • schrodinger.application.desmond.gui.EnsembleTab: Frame for the Ensemble tab of the Advanced Options dialog.
    • schrodinger.application.desmond.gui.IntegrationTab: Frame for the Integration tab of the Mdc Advanced Options dialogs
    • schrodinger.application.desmond.gui.MdcMiscTab: Frame for the Misc tab of Mdc Advanced Options dialogs.
      • schrodinger.application.desmond.gui.MinMiscTab: Frame for the Misc Tab of Advanced Options dialog of Minimization GUI.
    • schrodinger.application.desmond.gui.MinimizationTab: Frame for the Minimization tab of the Advanced Options dialog.
    • schrodinger.application.desmond.gui.RestraintsTab: Frame for the Restraints tab of the Advanced Options dialog
    • schrodinger.application.desmond.gui._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
      • schrodinger.application.desmond.gui.MdcAdvancedDialog: Advanced Options dialog for Mdc Desmond panels
      • schrodinger.application.desmond.gui.MinAdvancedDialog: Advanced Minimization options dialog for Desmond panels
  • schrodinger.structure._Molecule: A class used to return molecule information when iterating over molecules in a Structure object.
  • schrodinger.job.queue._MultiJobFinalizer: A class to allow specification of a function to be invoked when the final job of a group completes successfully.
  • schrodinger.application.desmond.ffiostructure._OtherBlock
    • schrodinger.application.desmond.ffiostructure._FEPIOOtherBlock: hash(x)
    • schrodinger.application.desmond.ffiostructure._FFIOOtherBlock: hash(x)
  • schrodinger.application.desmond.ffiostructure._OtherBlockContainer: The class to provide access to other block instances.
    • schrodinger.application.desmond.ffiostructure._FEPIOOtherBlockContainer
    • schrodinger.application.desmond.ffiostructure._FFIOOtherBlockContainer
  • schrodinger.trajectory.analysis._PBCMeasureMananger: A class to measure distance, angle, dihedral and planar angle under periodic boundary conditions.
  • schrodinger.ui.picking._PickToggle: Base class for picking toggles.
    • schrodinger.ui.picking.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
    • schrodinger.ui.picking.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
  • schrodinger.trajectory.analysis._RamachandranCallback: This class implements a callback to print information about selected Ramachandran plot points.
  • schrodinger.structure._Residue: A class which is returned by the ResidueIterator and contains information about the residue including the atoms which make it up.
  • schrodinger.structure._ResidueIterator: Residue iterator.
  • schrodinger.structure._Ring: Class representing a ring.
  • schrodinger.structure._RingEdgeIterator: Iterates over edges(bonds) of a _Ring.
  • schrodinger.protein.rotamers._Rotamer: A single instance of a rotamer - represents a set of CHI angle values
  • schrodinger.protein.rotamers._RotamerIterator: Container for the rotamers which are associated with a particular residue type
  • schrodinger.ui.widgettable._Row: Row of a table
  • schrodinger.application.desmond.fep_gui._ProMut._Site
  • schrodinger.structure._StructureAtom: A class to make access of mmct atoms properties more pythonic.
  • schrodinger.structure._StructureAtomContainer: The class to provide access to _StructureAtom instances.
  • schrodinger.structure._StructureBond: A class for pythonic access to bond properties.
  • schrodinger.structure._StructureBondContainer: The class to provide access to _StructureBond instances for each bond in the structure.
  • schrodinger.structure._StructureChainIterator: Class for iterating over chains in a Structure.
  • schrodinger.structure._StructureDeleter: A resource cleanup class for a single Structure.
  • schrodinger.structure._StructureManager: A class to handle Structure life-cycle events: initialization, termination, and deletion.
  • schrodinger.structure._StructureMoleculeIterator: Iterates over _Molecule in a Structure.
  • schrodinger.structure._StructureRingIterator: Container for all rings in the Structure.
  • threading._Verbose
    • threading.Thread
      • schrodinger.trajectory.rmsd2d.FrameLoader: A multi-threading class to load trajectory frame.
      • schrodinger.trajectory.rmsd2d.RMSDThreading
  • schrodinger.application.desmond.cmj._create_param_when_needed
  • schrodinger.application.desmond.config._create_when_needed
  • schrodinger.application.desmond.envir._create_when_needed
  • basestring: Type basestring cannot be instantiated; it is the base for str and unicode.
    • str: str(object) -> string
      • schrodinger.application.jaguar.output.CaseInsensitiveString: A class that behaves like a regular string except that comparisons are done on a case insensitive basis.
      • schrodinger.utils.sea.Key: An instance of this class will be used as the key of the Map class (see below).
  • schrodinger.application.desmond.enhsamp.binding
  • dict: dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.
    • collections.OrderedDict: Dictionary that remembers insertion order
      • schrodinger.application.bioluminate.protein.OrderedResidueDict: Creates an ordered dictionary for residues in a structure
    • schrodinger.project.PropertyDictionary: A dictionary of properties which can be indexed by dataname or column name (the name visible in the project).
    • configobj.Section: A dictionary-like object that represents a section in a config file.
      • configobj.ConfigObj: An object to read, create, and write config files.
        • schrodinger.application.inputconfig.InputConfig: Parse keyword-value input files and make the settings available in a dictionary-like fashion.
          • schrodinger.application.glide.glide.GlideJob: Class for writing Glide input files - either Gridgen or Docking.
            • schrodinger.application.glide.glide.Dock: Class for generating Glide docking input files.
            • schrodinger.application.glide.glide.Gridgen: Class for writing Glide Grid Generation input files.
          • schrodinger.application.prime.input.Prime: Class for reading and writing simplified Prime input files.
            • schrodinger.application.bioluminate.protein.PrimeConfig: Class containing the methods to write Prime input files.
          • schrodinger.application.macromodel.input._MacroModel: Class for reading and writing simplified MacroModel input files.
            • schrodinger.application.macromodel.input.ConfSearch: A special class for dealing with Conformation Search jobs.
            • schrodinger.application.macromodel.input.EmbraceConfSearch: A special class for dealing with Embrace Conformation Search jobs.
            • schrodinger.application.macromodel.input.EmbraceMinimization: A special class for dealing with Enbrace Minimization jobs.
            • schrodinger.application.macromodel.input.EnergyListing: A special class for dealing with Energy Listing jobs.
            • schrodinger.application.macromodel.input.Minimization: A special class for dealing with Minimization jobs.
            • schrodinger.application.macromodel.input.Minta: A special class for dealing with Minta jobs.
            • schrodinger.application.macromodel.input.RCE: A special class for dealing with RCE jobs.
    • schrodinger.application.jaguar.output.ZVariables: A class to store Z-variables and their values, generated in scan jobs.
    • schrodinger.maestro.maestro.property_dict: A dictionary of properties which can be indexed by dataname or column name (the name visible in the project).
  • float: float(x) -> floating point number
  • int: int(x[, base]) -> integer
    • PyQt4.QtGui.QFileDialog.AcceptMode
    • PyQt4.QtGui.QAction.ActionEvent
    • PyQt4.QtGui.QMovie.CacheMode
    • PyQt4.QtGui.QGraphicsView.CacheModeFlag
    • PyQt4.QtGui.QAbstractItemView.CursorAction
    • PyQt4.QtGui.QDialog.DialogCode
    • PyQt4.QtGui.QFileDialog.DialogLabel
    • PyQt4.QtGui.QProgressBar.Direction
    • PyQt4.QtGui.QMainWindow.DockOption
    • PyQt4.QtGui.QDockWidget.DockWidgetFeature
    • PyQt4.QtGui.QAbstractItemView.DragDropMode
    • PyQt4.QtGui.QGraphicsView.DragMode
    • PyQt4.QtGui.QAbstractItemView.DropIndicatorPosition
    • PyQt4.QtGui.QLineEdit.EchoMode
    • PyQt4.QtGui.QAbstractItemView.EditTrigger
    • PyQt4.QtGui.QAbstractItemDelegate.EndEditHint
    • PyQt4.QtGui.QFileDialog.FileMode
    • PyQt4.QtGui.QListView.Flow
    • PyQt4.QtGui.QFileIconProvider.IconType
    • PyQt4.QtGui.QComboBox.InsertPolicy
    • PyQt4.QtGui.QListView.LayoutMode
    • PyQt4.QtGui.QAction.MenuRole
    • PyQt4.QtGui.QListView.Movement
    • PyQt4.QtGui.QMovie.MovieState
    • PyQt4.QtGui.QGraphicsView.OptimizationFlag
    • PyQt4.QtGui.QFileDialog.Option
    • PyQt4.QtGui.QPaintDevice.PaintDeviceMetric
    • PyQt4.QtGui.QAction.Priority
    • PyQt4.QtGui.QWidget.RenderFlag
    • PyQt4.QtGui.QListView.ResizeMode
    • PyQt4.QtGui.QAbstractItemView.ScrollHint
    • PyQt4.QtGui.QAbstractItemView.ScrollMode
    • PyQt4.QtGui.QAbstractItemView.SelectionBehavior
    • PyQt4.QtGui.QAbstractItemView.SelectionMode
    • PyQt4.QtGui.QFrame.Shadow
    • PyQt4.QtGui.QFrame.Shape
    • PyQt4.QtGui.QComboBox.SizeAdjustPolicy
    • PyQt4.QtGui.QAction.SoftKeyRole
    • PyQt4.QtGui.QValidator.State
    • PyQt4.QtGui.QAbstractItemView.State
    • PyQt4.QtGui.QFrame.StyleMask
    • PyQt4.QtGui.QFileDialog.ViewMode
    • PyQt4.QtGui.QListView.ViewMode
    • PyQt4.QtGui.QGraphicsView.ViewportAnchor
    • PyQt4.QtGui.QGraphicsView.ViewportUpdateMode
  • schrodinger.application.jaguar.output.line_enumerate: A simple wrapper class to keep track of the line iteration count.
  • list: list() -> new empty list list(iterable) -> new list initialized from iterable's items
    • schrodinger.application.desmond.mdkey.List
    • schrodinger.utils.sea.List: This class represents the "list" parameters in a config file.
  • sip.simplewrapper
    • PyQt4.QtGui.QGraphicsView.CacheMode: QGraphicsView.CacheMode(QGraphicsView.CacheMode) QGraphicsView.CacheMode(int) QGraphicsView.CacheMode()
    • PyQt4.QtGui.QMainWindow.DockOptions: QMainWindow.DockOptions(QMainWindow.DockOptions) QMainWindow.DockOptions(int) QMainWindow.DockOptions()
    • PyQt4.QtGui.QDockWidget.DockWidgetFeatures: QDockWidget.DockWidgetFeatures(QDockWidget.DockWidgetFeatures) QDockWidget.DockWidgetFeatures(int) QDockWidget.DockWidgetFeatures()
    • PyQt4.QtGui.QAbstractItemView.EditTriggers: QAbstractItemView.EditTriggers(QAbstractItemView.EditTriggers) QAbstractItemView.EditTriggers(int) QAbstractItemView.EditTriggers()
    • PyQt4.QtGui.QGraphicsView.OptimizationFlags: QGraphicsView.OptimizationFlags(QGraphicsView.OptimizationFlags) QGraphicsView.OptimizationFlags(int) QGraphicsView.OptimizationFlags()
    • PyQt4.QtGui.QFileDialog.Options: QFileDialog.Options(QFileDialog.Options) QFileDialog.Options(int) QFileDialog.Options()
    • PyQt4.QtGui.QFileIconProvider: QFileIconProvider()
      • schrodinger.ui.qt.filedialog.PhaseDatabaseIconProvider: Class to ensure that projects get the proper icon in the file open dialog, and also are labeled as type "Project"
      • schrodinger.ui.qt.filedialog._CustomIconProvider: Class to ensure that Schrodinger file (and directory) types get a proper icon in the QFileDialog.
    • PyQt4.QtGui.QPaintDevice: QPaintDevice()
      • PyQt4.QtGui.QWidget: QWidget(QWidget parent=None, Qt.WindowFlags flags=0)
        • schrodinger.application.desmond.gui.AdvOptionsFrame: Frame for the "Advanced Options" button.
        • schrodinger.application.desmond.gui.EnsembleClassFrame: Frame that includes the Ensemble class pull-down menu and the entry fields correspondint to it.
        • schrodinger.application.desmond.gui.EnsembleTab: Frame for the Ensemble tab of the Advanced Options dialog.
        • schrodinger.application.desmond.cwidget.EntryField: A special composite widget which contains a labeled line edit field.
        • schrodinger.application.desmond.cwidget.FileEntry: Class combining a QLabel, QLineEdit, and a QPushButton (Browse...).
        • schrodinger.application.desmond.fep_gui.HelpLabel: A special composite widget which contains 2 help labels.
        • schrodinger.application.bioluminate.bwidgets.ImportWidget
        • schrodinger.application.desmond.gui.IntegrationTab: Frame for the Integration tab of the Mdc Advanced Options dialogs
        • schrodinger.application.desmond.gui.InteractionTab: Frame for the Interaction frame of the Advanced Options dialog.
        • schrodinger.ui.ligfilter.LigfilterFrame: Frame for setting up Ligfilter jobs, including property/SMARTS criteria and new definitions.
        • schrodinger.application.desmond.gui.MdcMiscTab: Frame for the Misc tab of Mdc Advanced Options dialogs.
          • schrodinger.application.desmond.gui.MinMiscTab: Frame for the Misc Tab of Advanced Options dialog of Minimization GUI.
        • schrodinger.application.desmond.gui.MinimizationTab: Frame for the Minimization tab of the Advanced Options dialog.
        • schrodinger.application.desmond.gui.OutputTab: Frame for the Output tab of the Advanced Options dialog
        • PyQt4.QtGui.QAbstractButton: QAbstractButton(QWidget parent=None)
          • PyQt4.QtGui.QCheckBox: QCheckBox(QWidget parent=None) QCheckBox(QString, QWidget parent=None)
            • schrodinger.application.desmond.fep_gui.PickAtomToggle: Pick atom widget with a precommand feature.
            • schrodinger.application.desmond.fep_gui.PickBondToggle: Pick bond widget with a precommand feature.
          • PyQt4.QtGui.QPushButton: QPushButton(QWidget parent=None) QPushButton(QString, QWidget parent=None) QPushButton(QIcon, QString, QWidget parent=None)
            • schrodinger.application.bioluminate.bwidgets.QuickHelpButton: A help button that has a blue gradient
        • PyQt4.QtGui.QComboBox: QComboBox(QWidget parent=None)
          • schrodinger.application.desmond.fep_gui.MultiSelectComboBox
        • PyQt4.QtGui.QDialog: QDialog(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog: Modal dialog window that allows users to set active databases.
          • schrodinger.ui.ligfilter.AddDefinitionDialog: Frame for generating a pattern definition.
          • schrodinger.ui.chooseligand.ChooseLigandDialog
          • schrodinger.application.bioluminate.pml_menus.ColorChooserPanel: A window that lets the user choose a Maestro color.
          • schrodinger.antibody_db_manage_gui.ColumnSelectDialog: Dialog that allows the user to specify what columns to search on
          • schrodinger.ui.ligfilter.DefinitionViewerDialog: Frame containing a text box with a text display of the definition.
          • schrodinger.application.bioluminate.propfilter.PropFilterDialog: Panel to allow the user to define criteria for filtering property values
          • PyQt4.QtGui.QFileDialog: QFileDialog(QWidget, Qt.WindowFlags) QFileDialog(QWidget parent=None, QString caption=QString(), QString directory=QString(), QString filter=QString())
            • schrodinger.ui.qt.filedialog.FileDialog: File browser dialog with custom sidebar.
              • schrodinger.application.bioluminate.bwidgets.SequenceFileDialog: Custom class to handle opening files related to sequences.
                • schrodinger.application.bioluminate.bwidgets.TemplateFileDialog: File dialog specific to templates
            • schrodinger.ui.qt.filedialog.PhaseDatabaseOpenDialog: A file dialog tailored to opening Phase databases.
            • schrodinger.ui.qt.filedialog.ProjectOpenDialog: A file dialog tailored to opening Projects.
          • schrodinger.application.desmond.cwidget.StartDialogBase
            • schrodinger.application.desmond.cwidget.StartDialog1
            • schrodinger.application.desmond.cwidget.StartDialog2
          • schrodinger.application.bioluminate.propfilter.ValueSelectionDialog: A SFilteredListWidget that allows the user to select certain values of a property for the criterion.
          • schrodinger.application.desmond.gui._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
            • schrodinger.application.desmond.gui.MdcAdvancedDialog: Advanced Options dialog for Mdc Desmond panels
            • schrodinger.application.desmond.gui.MinAdvancedDialog: Advanced Minimization options dialog for Desmond panels
        • PyQt4.QtGui.QDockWidget: QDockWidget(QString, QWidget parent=None, Qt.WindowFlags flags=0) QDockWidget(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget: The dock widget that can set a ViewerWindow as the main widget.
        • PyQt4.QtGui.QFrame: QFrame(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.application.desmond.fep_gui.HorizontalBar
          • schrodinger.application.desmond.gui.HorizontalBar
          • schrodinger.ui.qt.appframework.JobInputFrame: An application input source selection widget.
          • PyQt4.QtGui.QAbstractScrollArea: QAbstractScrollArea(QWidget parent=None)
            • PyQt4.QtGui.QAbstractItemView: QAbstractItemView(QWidget parent=None)
              • PyQt4.QtGui.QListView: QListView(QWidget parent=None)
                • PyQt4.QtGui.QListWidget: QListWidget(QWidget parent=None)
                  • schrodinger.ui.qt.swidgets.SListWidget: A QListWidget that can set its items and set up a callback at creation.
                    • schrodinger.ui.qt.swidgets.SFilteredListWidget: An SListWidget with an additional line edit that can be used to filter the items within the ListWidget
                      • schrodinger.application.bioluminate.propfilter.SelectingFilteredListWidget: A QListWidget that contains a edit to allow the user to filter the contents of the widget.
              • PyQt4.QtGui.QTableView: QTableView(QWidget parent=None)
                • schrodinger.ui.qt.table.DataViewerTable
                  • schrodinger.ui.qt.table.SEasySDTable: A simple class that automatically sets up the table/model/delegate trio for a table object
                    • schrodinger.antibody_db_manage_gui.Editable: A table class that allows editing of cells
                • PyQt4.QtGui.QTableWidget: QTableWidget(QWidget parent=None) QTableWidget(int, int, QWidget parent=None)
                  • schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable: Table that is used to show and carry out actions on all databases loaded by user.
            • PyQt4.QtGui.QGraphicsView: QGraphicsView(QWidget parent=None) QGraphicsView(QGraphicsScene, QWidget parent=None)
              • schrodinger.ui.sketcher.sketcherView
          • PyQt4.QtGui.QLabel: QLabel(QWidget parent=None, Qt.WindowFlags flags=0) QLabel(QString, QWidget parent=None, Qt.WindowFlags flags=0)
            • schrodinger.application.desmond.fep_gui.AdvLabel: A mutli-line label with small, bold text.
            • schrodinger.application.desmond.cwidget.AdvLabel: A mutli-line label with small, bold text.
            • schrodinger.application.bioluminate.pml_menus.ColorLabel: A label that shows off the color each element will be colored if this menu item is chosen.
            • schrodinger.application.desmond.cwidget.DesresTradeMark: Class for drawing the Desmond trademark logo to the GUI.
          • PyQt4.QtGui.QSplitter: QSplitter(QWidget parent=None) QSplitter(Qt.Orientation, QWidget parent=None)
            • schrodinger.ui.sequencealignment.sequence_viewer.SequenceViewer: The sequence viewer widget displays and manipulates sequences and associated data.
              • schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer: Creates a sequence viewer that can be opened by an action or added to a main window as a dockable item.
          • schrodinger.application.bioluminate.protein_report_widget.ReportFrame: A QtGui.QFrame that contains a Protein Report
            • schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart: A Protein Report widget that can deal with multiple protein structures and also has a slider chart that can be used to select residues.
          • schrodinger.application.bioluminate.pml_menus.ResultsWindow
          • schrodinger.application.bioluminate.sliderchart.SliderPlot: A chart that contains four lines the user can slide to select a region of the chart.
        • PyQt4.QtGui.QGroupBox: QGroupBox(QWidget parent=None) QGroupBox(QString, QWidget parent=None)
          • schrodinger.application.desmond.gui.AtomGroupFrame: Frame for the "Atom group" box of the Misc tab of the Advanced Options dialog.
          • schrodinger.application.desmond.gui.InputGroup: Group Frame for showing the widgets for loading the system model.
          • schrodinger.application.desmond.gui.MinOutputFrame: Group box "Output" of the "Minimization" tab of Advanced Options dialog.
          • schrodinger.application.desmond.gui.MinimizerFrame: Group box "Minimizer" of the "Minimization" tab of Advanced Options dialog.
          • schrodinger.application.desmond.gui.RandVelFrame: Frame for the "Randomize velocities" group of the Misc tab of Advanced dialog.
          • schrodinger.application.desmond.gui._BaseGroup: Enherited by MdGroup and MinimizeGroup, so therefore by all Simulation frames
            • schrodinger.application.desmond.gui.MdGroup: Molecular Dynamics group
          • schrodinger.application.desmond.fep_gui._ProtItem: Frame for each checkable group of the second tab of the panel (Plan Calculation).
          • schrodinger.application.desmond.cwidget._SdIncorpFrame: The incorporation (output) frame of the start dialog.
          • schrodinger.application.desmond.cwidget._SdJobFrame: Frame for the master job options
          • schrodinger.application.desmond.cwidget._SdMasterjob
          • schrodinger.application.desmond.cwidget._SdSubjobFrame
        • PyQt4.QtGui.QLineEdit: QLineEdit(QWidget parent=None) QLineEdit(QString, QWidget parent=None)
          • schrodinger.application.bioluminate.bwidgets.NumericLineEdit: A QtGui.QLineEdit with a builtin validator for floats or integers.
        • PyQt4.QtGui.QMainWindow: QMainWindow(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.ui.qt.appframework.AppFramework: The AppFramework class is basically a hull for applications.
            • schrodinger.antibody_db_manage_gui.AdvancedOptionsPanel: The panel to change advanced options
            • schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog: A class which displays a dialog with a plot of the statistics for the most recent clustering
            • schrodinger.antibody_db_manage_gui.DBManagePanel: The Main Panel Class
            • schrodinger.application.canvas.clustergui.DendrogramPlotDialog: A class which displays a dialog with a plot of the dendrogram from the most recent clustering
            • schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog: A class which displays a dialog with a plot of the distance matrix associated with the most recent clustering
            • schrodinger.application.desmond.gui.GuiApp: Base class of several Desmond panel GUI's (see its subclasses below).
            • schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer: The Main Panel Class
            • schrodinger.ui.chooseligand.TestApp: Class for testing this module.
            • schrodinger.ui.qt.appframework.TestApp: Class for testing AppFramework outside of Maestro.
            • schrodinger.application.desmond.fep_gui._App: Class shared by Desmond and Mcpro applications
              • schrodinger.application.desmond.fep_gui.DesmondApp: Class shared by all Desmond panels.
              • schrodinger.application.desmond.fep_gui.McproApp: Class shared by all Mcpro panels
          • schrodinger.application.bioluminate.ssv.viewer.ViewerWindow: Provides the SimplifiedSequenceViewer with a window to occupy.
          • schrodinger.ui.sketcher.sketcher
        • PyQt4.QtGui.QMenu: QMenu(QWidget parent=None) QMenu(QString, QWidget parent=None)
          • schrodinger.application.bioluminate.pml_menus.ColorByElementSubMenu: The Color by Element submenu
          • schrodinger.application.bioluminate.pml_menus.PMLMenu: The base menu class we subclass from
            • schrodinger.application.bioluminate.pml_menus.ActionMenu: The Action menu
            • schrodinger.application.bioluminate.pml_menus.AroundExpandSubMenu: The modify-around submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.AsMenu: The Show->As submenu
            • schrodinger.application.bioluminate.pml_menus.AutoColorSubMenu: The Color menu
            • schrodinger.application.bioluminate.pml_menus.ColorChainSubMenu: The ColorChainSubMenu menu
            • schrodinger.application.bioluminate.pml_menus.ColorMenu: The Color menu
            • schrodinger.application.bioluminate.pml_menus.ColorSpectrumSubMenu: The ColorSpectrumSubMenu menu
            • schrodinger.application.bioluminate.pml_menus.ColorSubstructureSubMenu: The ColorSubstructureSubMenu menu
            • schrodinger.application.bioluminate.pml_menus.CompleteSubMenu: The modify-complete submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.ComputeSubMenu: The Action Compute submenu
            • schrodinger.application.bioluminate.pml_menus.EntrySubMenu: A submenu that lists all enabled Entry objects
            • schrodinger.application.bioluminate.pml_menus.ExcludeSubMenu: The modify-exclude submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.ExtendSubMenu: The modify-extend submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.FindPCSubMenu: The Find Polar Contacts submenu
            • schrodinger.application.bioluminate.pml_menus.GenSelectionSubMenu: The Action Generate Selection submenu
            • schrodinger.application.bioluminate.pml_menus.GenSymMatesSubMenu: The Action Generate Symmetry Mates submenu
            • schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu: The submenu that contains all the main actions used for most context menus
              • schrodinger.application.bioluminate.pml_menus.ObjectFreeContextSubMenu: The GeneralContextSubMenu for a right-click that is not on an object
              • schrodinger.application.bioluminate.pml_menus.SubstructureContextSubMenu: The GeneralContextSubMenu for a right-click that is on an atom
            • schrodinger.application.bioluminate.pml_menus.GenerateSubMenu: The Action Generate submenu
            • schrodinger.application.bioluminate.pml_menus.HideHydrogenSubMenu: The Hide Hydrogen submenu
            • schrodinger.application.bioluminate.pml_menus.HideMenu: The Hide menu
            • schrodinger.application.bioluminate.pml_menus.HydrogenSubMenu: The Action Hydrogen submenu
            • schrodinger.application.bioluminate.pml_menus.IncludeSubMenu: The modify-include submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.InvertSubMenu: The modify-invert submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.LabelAtomIdentSubMenu: The Label Atom Identifiers submenu
            • schrodinger.application.bioluminate.pml_menus.LabelMenu: The Label menu
            • schrodinger.application.bioluminate.pml_menus.LabelOtherSubMenu: The Label Other Properties submenu
            • schrodinger.application.bioluminate.pml_menus.LigandSitesSubMenu: The Action-Preset-Ligand Sites submenu
            • schrodinger.application.bioluminate.pml_menus.ModifySubMenu: The modify submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.PMLContextMenu: The base menu class we subclass from for context menus
              • schrodinger.application.bioluminate.pml_menus.AtomContextMenu: The context menu for right-clicks on non-selected atoms
              • schrodinger.application.bioluminate.pml_menus.SelectedAtomContextMenu: The context menu for right-clicks on selected atoms
              • schrodinger.application.bioluminate.pml_menus.SpaceContextMenu: The context menu for right-clicks in space
            • schrodinger.application.bioluminate.pml_menus.PolarContactsSubMenu: The Polar Contacts submenu
            • schrodinger.application.bioluminate.pml_menus.PresetSubMenu: The Preset submenu
            • schrodinger.application.bioluminate.pml_menus.RestrictSubMenu: The modify-restrict submenu of the action menu
            • schrodinger.application.bioluminate.pml_menus.SelectedAtomContextActionSubMenu: The submenu that allows the user to enable/disable individual objects
            • schrodinger.application.bioluminate.pml_menus.SelectionSubMenu: A submenu that lists all enabled Entry objects
            • schrodinger.application.bioluminate.pml_menus.ShowMenu: The Show menu
            • schrodinger.application.bioluminate.pml_menus.SurfaceAreaSubMenu: The Action Surface Area submenu
            • schrodinger.application.bioluminate.pml_menus.ToggleStateSubMenu: The submenu that allows the user to enable/disable individual objects
          • schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu: A submenu that shows the most recently chosen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
            • schrodinger.application.bioluminate.pml_menus.RecentCarbonColorSubMenu: A submenu that shows the most recently chosen carbon colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
            • schrodinger.application.bioluminate.pml_menus.RecentHydrogenColorSubMenu: A submenu that shows the most recently chosen hydrogen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
            • schrodinger.application.bioluminate.pml_menus.RecentObjectColorSubMenu: A submenu that shows the most recently chosen object colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
          • schrodinger.application.bioluminate.pml_menus.ShowOrganicMenu: The Show->Organic submenus
          • schrodinger.application.bioluminate.pml_menus.ShowSubstructureMenu: The Show->substructure submenus
        • PyQt4.QtGui.QProgressBar: QProgressBar(QWidget parent=None)
          • schrodinger.ui.qt.appframework.CustomProgressBar: Class for a custom progress bar (at the bottom of some panels).
        • PyQt4.QtGui.QToolBar: QToolBar(QString, QWidget parent=None) QToolBar(QWidget parent=None)
          • schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar: Get the toolbar that has the combobox with the antibody numering schemes.
          • schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar: A toolbar associated with the viewer that will handle display options.
          • schrodinger.application.bioluminate.ssv.toolbars.FindToolBar: Create an instance of the "Find Pattern" toolbar from the MSV.
          • schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar: Get the toolbar that has the import dialogs.
          • schrodinger.ui.sketcher.sketcherGUIMultiColumnToolBar
        • schrodinger.application.desmond.gui.RelaxFrame: Frame that includes the "Relax model..." check box and the relaxation protocol entry field.
        • schrodinger.application.desmond.gui.RestraintsTab: Frame for the Restraints tab of the Advanced Options dialog
        • schrodinger.application.bioluminate.bwidgets.RowActionItem: Custom widget to be used in a table cell.
        • schrodinger.application.desmond.gui.SimOptionsFrame: Responsible for drawing the simulation options widgets, including Simulation time and Recording intervals.
        • schrodinger.application.desmond.fep_gui._DesmondProt: Frame for the second tab ("Plan Calculation") of the Desmond GUIs.
        • schrodinger.ui.qt.appframework._EntryField: A special composite widget which contains a labeled line edit field.
        • schrodinger.application.desmond.fep_gui._LigMut: Class of the "Ligand Functional Group Mutation by FEP" panel.
        • schrodinger.application.desmond.fep_gui._McproProt: Frame for the second tab ("Plan Calculation") of the Mcpro GUIs.
        • schrodinger.application.desmond.fep_gui._Pert: Frame for the bottom part of the "Plan Calculation" tab of Mcpro GUIs.
        • schrodinger.application.desmond.fep_gui._ProMut: Main code of the Protein Residue Mutation GUI
        • schrodinger.application.desmond.fep_gui._RingMut
        • schrodinger.application.desmond.cwidget._SdDetailFrame: Frame for the section that gets shown when the "Detail" button is toggled on.
    • PyQt4.QtGui.QWidget.RenderFlags: QWidget.RenderFlags(QWidget.RenderFlags) QWidget.RenderFlags(int) QWidget.RenderFlags()
    • sip.wrapper
      • schrodinger.infra._canvas2d.ChemViewAnnotator
        • schrodinger.application.lid.lid2d.annotators.GetLabelBBXAnnotator
        • schrodinger.application.lid.lid2d.annotators.LidAnnotator
        • schrodinger.application.lid.lid2d.annotators.SetCoordinateAnnotator
      • PyQt4.QtCore.QObject: QObject(QObject parent=None)
        • PyQt4.QtGui.QAbstractItemDelegate: QAbstractItemDelegate(QObject parent=None)
          • PyQt4.QtGui.QItemDelegate: QItemDelegate(QObject parent=None)
            • schrodinger.application.desmond.gui.AtomGroupDelegate: Class for allowing the data in the AtomGroupModel to be modified.
            • schrodinger.ui.qt.table.GenericViewerDelegate: This is the class that handles the actual drawing of data.
              • schrodinger.ui.qt.table.StructureDataViewerDelegate: A table that can display both 2-D structures and data.
                • schrodinger.antibody_db_manage_gui.EditableDelegate: The table delegate, modified to shade the background of read-only cells, align data types accordingly and store data in the model when the user edits a cell.
            • schrodinger.application.desmond.gui.PosResDelegate: Class for allowing the data in the PosResModel to be modified
            • schrodinger.application.desmond.fep_gui.ResiduesDelegate: Class for allowing the data in the ResiduesModel to be modified by the user through pull-down menus in the cells.
            • schrodinger.application.desmond.gui.TempItemDelegate: Class for allowing the data in the TableModel to be modified.
        • PyQt4.QtCore.QAbstractItemModel: QAbstractItemModel(QObject parent=None)
          • PyQt4.QtCore.QAbstractListModel: QAbstractListModel(QObject parent=None)
            • schrodinger.ui.ligfilter.CriteriaListModel: Class for storing the criteria list information.
            • schrodinger.application.bioluminate.propfilter.CriteriaListModel: Class for storing the criteria list information.
          • PyQt4.QtGui.QAbstractProxyModel: QAbstractProxyModel(QObject parent=None)
            • PyQt4.QtGui.QSortFilterProxyModel: QSortFilterProxyModel(QObject parent=None)
              • schrodinger.antibody_db_manage_gui.EditableProxyModel: A proxy model that allows editing and custom filtering
          • PyQt4.QtCore.QAbstractTableModel: QAbstractTableModel(QObject parent=None)
            • schrodinger.application.desmond.gui.AtomGroupModel: Class for storing the window table information.
            • schrodinger.ui.chooseligand.ChooseLigandModel
            • schrodinger.application.bioluminate.protein_report_widget.DataModel: Class for storing the table information.
              • schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart: A subclass of DataModel that calls a sort callback when sorting
            • schrodinger.application.desmond.fep_gui.PathModel: Class for storing table information.
            • schrodinger.ui.ligfilter.PatternModel: Class for strring patterns (definitions) and their groups
            • schrodinger.application.desmond.gui.PosResModel: Class for storing the window table information.
            • schrodinger.application.desmond.fep_gui.ResiduesModel: Class for storing the residues table information.
            • schrodinger.application.desmond.fep_gui.StrucListModel: Class for storing table information.
            • schrodinger.application.desmond.gui.TableModel: Class for storing the window table information.
            • schrodinger.ui.qt.table.ViewerModel
              • schrodinger.ui.qt.table.StructureDataViewerModel: A table model that handles 2-D structures and data.
                • schrodinger.antibody_db_manage_gui.EditableModel: A model that allows the user to edit cells in some columns of the table.
        • PyQt4.QtGui.QAction: QAction(QObject) QAction(QString, QObject) QAction(QIcon, QString, QObject)
          • schrodinger.application.bioluminate.pml_menus.MAction: A QAction that performs a Maestro command
            • schrodinger.application.bioluminate.pml_menus.AddHydrogens
            • schrodinger.application.bioluminate.pml_menus.AutoColorObjects
              • schrodinger.application.bioluminate.pml_menus.AutoColorCarbons
            • schrodinger.application.bioluminate.pml_menus.AutoCycleColor
              • schrodinger.application.bioluminate.pml_menus.AutoCycleCarbonColor
            • schrodinger.application.bioluminate.pml_menus.Center
            • schrodinger.application.bioluminate.pml_menus.Clean
            • schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor
              • schrodinger.application.bioluminate.pml_menus.ColorCalphasByBFactor
            • schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum
              • schrodinger.application.bioluminate.pml_menus.ColorCalphasBySpectrum
              • schrodinger.application.bioluminate.pml_menus.ColorCarbonsBySpectrum
            • schrodinger.application.bioluminate.pml_menus.ColorChainbows
            • schrodinger.application.bioluminate.pml_menus.ColorChains
              • schrodinger.application.bioluminate.pml_menus.ColorChainsByCalpha
              • schrodinger.application.bioluminate.pml_menus.ColorChainsByCarbon
            • schrodinger.application.bioluminate.pml_menus.ColorHNOS
            • schrodinger.application.bioluminate.pml_menus.ComputeSurfaceArea
            • schrodinger.application.bioluminate.pml_menus.CountAtoms
            • schrodinger.application.bioluminate.pml_menus.CreateEntry
            • schrodinger.application.bioluminate.pml_menus.CustomColor
              • schrodinger.application.bioluminate.pml_menus.ColorCarbons
              • schrodinger.application.bioluminate.pml_menus.ColorHydrogens
              • schrodinger.application.bioluminate.pml_menus.ColorObject
            • schrodinger.application.bioluminate.pml_menus.DeleteAll
            • schrodinger.application.bioluminate.pml_menus.DeleteAtoms
            • schrodinger.application.bioluminate.pml_menus.DeleteProject
            • schrodinger.application.bioluminate.pml_menus.DeleteSelections
            • schrodinger.application.bioluminate.pml_menus.DeleteWS
            • schrodinger.application.bioluminate.pml_menus.Disable
            • schrodinger.application.bioluminate.pml_menus.Duplicate
            • schrodinger.application.bioluminate.pml_menus.ExcludeInorganicFromSelection
            • schrodinger.application.bioluminate.pml_menus.ExcludeOrganicFromSelection
            • schrodinger.application.bioluminate.pml_menus.ExcludePolymerFromSelection
            • schrodinger.application.bioluminate.pml_menus.ExcludeSolventFromSelection
            • schrodinger.application.bioluminate.pml_menus.ExcludeVisibleFromSelection
            • schrodinger.application.bioluminate.pml_menus.Expand: Expand the selection to the atoms around the ASL for this object
              • schrodinger.application.bioluminate.pml_menus.Around
            • schrodinger.application.bioluminate.pml_menus.Extend: Expand the selection to the atoms within X bonds of the ASL for this object
            • schrodinger.application.bioluminate.pml_menus.GenerateSelection: Select the atoms, then generate a selection object from them
              • schrodinger.application.bioluminate.pml_menus.GenerateInterfaceSelection
              • schrodinger.application.bioluminate.pml_menus.GenerateLigandSelection
              • schrodinger.application.bioluminate.pml_menus.GenerateSurfResSelection
            • schrodinger.application.bioluminate.pml_menus.GenerateSymmetryMates: Generate all the symmetry mates and show those within X angstroms
            • schrodinger.application.bioluminate.pml_menus.HideAllOthers
            • schrodinger.application.bioluminate.pml_menus.HideAtoms
            • schrodinger.application.bioluminate.pml_menus.HideEverything
            • schrodinger.application.bioluminate.pml_menus.HideHydrogens
            • schrodinger.application.bioluminate.pml_menus.HideLabel
            • schrodinger.application.bioluminate.pml_menus.HideMainChain
            • schrodinger.application.bioluminate.pml_menus.HideNonBonded
            • schrodinger.application.bioluminate.pml_menus.HidePolarHydrogens
            • schrodinger.application.bioluminate.pml_menus.HideRibbons
            • schrodinger.application.bioluminate.pml_menus.HideSideChain
            • schrodinger.application.bioluminate.pml_menus.HideSurface
            • schrodinger.application.bioluminate.pml_menus.HideSymmetryMates
            • schrodinger.application.bioluminate.pml_menus.HideWaters
            • schrodinger.application.bioluminate.pml_menus.IncludeVisibleInSelection
            • schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection: Invert or complete the selection within an object
              • schrodinger.application.bioluminate.pml_menus.SelectWithinAny
              • schrodinger.application.bioluminate.pml_menus.SelectWithinCalpha
              • schrodinger.application.bioluminate.pml_menus.SelectWithinChain
              • schrodinger.application.bioluminate.pml_menus.SelectWithinEntry
              • schrodinger.application.bioluminate.pml_menus.SelectWithinMolecule
              • schrodinger.application.bioluminate.pml_menus.SelectWithinResidue
            • schrodinger.application.bioluminate.pml_menus.LabelAtom: A QAction that performs labels atoms with the given label
            • schrodinger.application.bioluminate.pml_menus.LabelAtomByProp: Labels all atoms by a custom atom property
              • schrodinger.application.bioluminate.pml_menus.LabelAtomByEntryIndex
              • schrodinger.application.bioluminate.pml_menus.LabelAtomByMolIndex
              • schrodinger.application.bioluminate.pml_menus.LabelAtomByNumType
              • schrodinger.application.bioluminate.pml_menus.LabelAtomByOccupancy
              • schrodinger.application.bioluminate.pml_menus.LabelAtomByVDW
            • schrodinger.application.bioluminate.pml_menus.LabelAtomByStereo
            • schrodinger.application.bioluminate.pml_menus.LabelChains
            • schrodinger.application.bioluminate.pml_menus.LabelResidues
            • schrodinger.application.bioluminate.pml_menus.MakeProjectEntry: Copies the atoms into a new project entry and includes it in the workspace
            • schrodinger.application.bioluminate.pml_menus.Orient
            • schrodinger.application.bioluminate.pml_menus.Origin
            • schrodinger.application.bioluminate.pml_menus.PolarContactsObject
            • schrodinger.application.bioluminate.pml_menus.PolarContactsOnlyMainchain
            • schrodinger.application.bioluminate.pml_menus.PolarContactsOnlySidechain
            • schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyAtoms
            • schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyNonSolvent
            • schrodinger.application.bioluminate.pml_menus.PolarContactsToEntry
            • schrodinger.application.bioluminate.pml_menus.PolarContactsToEntryWithoutSolvent
            • schrodinger.application.bioluminate.pml_menus.PolarContactsWithSidechains
            • schrodinger.application.bioluminate.pml_menus.PolarContactsWithSolvent
            • schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutIntraMainchain
            • schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutMainchain
            • schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutSolvent
            • schrodinger.application.bioluminate.pml_menus.PresetAction: Base class for Preset Actions
              • schrodinger.application.bioluminate.pml_menus.AntibodyPreset
              • schrodinger.application.bioluminate.pml_menus.BAndSPreset
              • schrodinger.application.bioluminate.pml_menus.BFactorPreset
              • schrodinger.application.bioluminate.pml_menus.DefaultPreset
              • schrodinger.application.bioluminate.pml_menus.InterfacePreset
              • schrodinger.application.bioluminate.pml_menus.LigandPreset
              • schrodinger.application.bioluminate.pml_menus.PrettyPubPreset: Show the object as nice-looking cartoon ribbons
              • schrodinger.application.bioluminate.pml_menus.SimplePreset
              • schrodinger.application.bioluminate.pml_menus.TechnicalPreset
            • schrodinger.application.bioluminate.pml_menus.Quit
            • schrodinger.application.bioluminate.pml_menus.Ray: Use PyMOL to make a ray-traced image
            • schrodinger.application.bioluminate.pml_menus.Reinitialize
            • schrodinger.application.bioluminate.pml_menus.RemoveHydrogens
            • schrodinger.application.bioluminate.pml_menus.RemovePC
            • schrodinger.application.bioluminate.pml_menus.RemoveWaters
            • schrodinger.application.bioluminate.pml_menus.Rename
            • schrodinger.application.bioluminate.pml_menus.RestrictSelection: Restrict the selection to a specific object
              • schrodinger.application.bioluminate.pml_menus.ExcludeFromSelection
              • schrodinger.application.bioluminate.pml_menus.IncludeInSelection: Include a specific object in the selection
            • schrodinger.application.bioluminate.pml_menus.RestrictToInorganic
            • schrodinger.application.bioluminate.pml_menus.RestrictToOrganic
            • schrodinger.application.bioluminate.pml_menus.RestrictToPolymer
            • schrodinger.application.bioluminate.pml_menus.RestrictToSolvent
            • schrodinger.application.bioluminate.pml_menus.RestrictToVisible
            • schrodinger.application.bioluminate.pml_menus.Select
            • schrodinger.application.bioluminate.pml_menus.ShowBAndS
            • schrodinger.application.bioluminate.pml_menus.ShowCartoon
            • schrodinger.application.bioluminate.pml_menus.ShowLabel
            • schrodinger.application.bioluminate.pml_menus.ShowLines
              • schrodinger.application.bioluminate.pml_menus.ShowLigandLines
            • schrodinger.application.bioluminate.pml_menus.ShowNonBonded
              • schrodinger.application.bioluminate.pml_menus.ShowNonBondedSpheres
            • schrodinger.application.bioluminate.pml_menus.ShowRibbon
            • schrodinger.application.bioluminate.pml_menus.ShowSpheres
              • schrodinger.application.bioluminate.pml_menus.ShowLigandSpheres
            • schrodinger.application.bioluminate.pml_menus.ShowTubes
              • schrodinger.application.bioluminate.pml_menus.ShowLigandTubes
            • schrodinger.application.bioluminate.pml_menus.SumFormalCharge
            • schrodinger.application.bioluminate.pml_menus.SumPartialCharge
            • schrodinger.application.bioluminate.pml_menus.SurfaceRender: Base class for actions that render a surface
              • schrodinger.application.bioluminate.pml_menus.ShowMesh
              • schrodinger.application.bioluminate.pml_menus.ShowSurface
            • schrodinger.application.bioluminate.pml_menus.ToggleState: A MAction that toggles the enabled/disabled state of an object
            • schrodinger.application.bioluminate.pml_menus.Zoom
          • PyQt4.QtGui.QWidgetAction: QWidgetAction(QObject)
            • schrodinger.application.bioluminate.pml_menus.MWidgetAction: A QAction that performs a Maestro command
              • schrodinger.application.bioluminate.pml_menus.ColorBySubstructure
              • unreachable.CustomRecentColor
                • schrodinger.application.bioluminate.pml_menus.ColorRecentCarbons
                • schrodinger.application.bioluminate.pml_menus.ColorRecentHydrogens
                • schrodinger.application.bioluminate.pml_menus.ColorRecentObjects
              • schrodinger.application.bioluminate.pml_menus.CustomRecentColor
          • schrodinger.application.bioluminate.actions.factory.SAction: A QAction that enforces standards that are expected by some BioLuminate methods.
        • PyQt4.QtGui.QMovie: QMovie(QObject parent=None) QMovie(QIODevice, QByteArray format=QByteArray(), QObject parent=None) QMovie(QString, QByteArray format=QByteArray(), QObject parent=None)
          • schrodinger.application.bioluminate.bwidgets.LoadingIcon: Animates a "loading" icon that can be used by any Qt object that has the C{setIcon} method.
        • PyQt4.QtGui.QValidator: QValidator(QObject parent=None)
          • PyQt4.QtGui.QIntValidator: QIntValidator(QObject parent=None) QIntValidator(int, int, QObject)
            • schrodinger.application.desmond.cwidget.CpuValidator
        • PyQt4.QtGui.QWidget: QWidget(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.application.desmond.gui.AdvOptionsFrame: Frame for the "Advanced Options" button.
          • schrodinger.application.desmond.gui.EnsembleClassFrame: Frame that includes the Ensemble class pull-down menu and the entry fields correspondint to it.
          • schrodinger.application.desmond.gui.EnsembleTab: Frame for the Ensemble tab of the Advanced Options dialog.
          • schrodinger.application.desmond.cwidget.EntryField: A special composite widget which contains a labeled line edit field.
          • schrodinger.application.desmond.cwidget.FileEntry: Class combining a QLabel, QLineEdit, and a QPushButton (Browse...).
          • schrodinger.application.desmond.fep_gui.HelpLabel: A special composite widget which contains 2 help labels.
          • schrodinger.application.bioluminate.bwidgets.ImportWidget
          • schrodinger.application.desmond.gui.IntegrationTab: Frame for the Integration tab of the Mdc Advanced Options dialogs
          • schrodinger.application.desmond.gui.InteractionTab: Frame for the Interaction frame of the Advanced Options dialog.
          • schrodinger.ui.ligfilter.LigfilterFrame: Frame for setting up Ligfilter jobs, including property/SMARTS criteria and new definitions.
          • schrodinger.application.desmond.gui.MdcMiscTab: Frame for the Misc tab of Mdc Advanced Options dialogs.
            • schrodinger.application.desmond.gui.MinMiscTab: Frame for the Misc Tab of Advanced Options dialog of Minimization GUI.
          • schrodinger.application.desmond.gui.MinimizationTab: Frame for the Minimization tab of the Advanced Options dialog.
          • schrodinger.application.desmond.gui.OutputTab: Frame for the Output tab of the Advanced Options dialog
          • PyQt4.QtGui.QAbstractButton: QAbstractButton(QWidget parent=None)
            • PyQt4.QtGui.QCheckBox: QCheckBox(QWidget parent=None) QCheckBox(QString, QWidget parent=None)
              • schrodinger.application.desmond.fep_gui.PickAtomToggle: Pick atom widget with a precommand feature.
              • schrodinger.application.desmond.fep_gui.PickBondToggle: Pick bond widget with a precommand feature.
            • PyQt4.QtGui.QPushButton: QPushButton(QWidget parent=None) QPushButton(QString, QWidget parent=None) QPushButton(QIcon, QString, QWidget parent=None)
              • schrodinger.application.bioluminate.bwidgets.QuickHelpButton: A help button that has a blue gradient
          • PyQt4.QtGui.QComboBox: QComboBox(QWidget parent=None)
            • schrodinger.application.desmond.fep_gui.MultiSelectComboBox
          • PyQt4.QtGui.QDialog: QDialog(QWidget parent=None, Qt.WindowFlags flags=0)
            • schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog: Modal dialog window that allows users to set active databases.
            • schrodinger.ui.ligfilter.AddDefinitionDialog: Frame for generating a pattern definition.
            • schrodinger.ui.chooseligand.ChooseLigandDialog
            • schrodinger.application.bioluminate.pml_menus.ColorChooserPanel: A window that lets the user choose a Maestro color.
            • schrodinger.antibody_db_manage_gui.ColumnSelectDialog: Dialog that allows the user to specify what columns to search on
            • schrodinger.ui.ligfilter.DefinitionViewerDialog: Frame containing a text box with a text display of the definition.
            • schrodinger.application.bioluminate.propfilter.PropFilterDialog: Panel to allow the user to define criteria for filtering property values
            • PyQt4.QtGui.QFileDialog: QFileDialog(QWidget, Qt.WindowFlags) QFileDialog(QWidget parent=None, QString caption=QString(), QString directory=QString(), QString filter=QString())
              • schrodinger.ui.qt.filedialog.FileDialog: File browser dialog with custom sidebar.
                • schrodinger.application.bioluminate.bwidgets.SequenceFileDialog: Custom class to handle opening files related to sequences.
                  • schrodinger.application.bioluminate.bwidgets.TemplateFileDialog: File dialog specific to templates
              • schrodinger.ui.qt.filedialog.PhaseDatabaseOpenDialog: A file dialog tailored to opening Phase databases.
              • schrodinger.ui.qt.filedialog.ProjectOpenDialog: A file dialog tailored to opening Projects.
            • schrodinger.application.desmond.cwidget.StartDialogBase
              • schrodinger.application.desmond.cwidget.StartDialog1
              • schrodinger.application.desmond.cwidget.StartDialog2
            • schrodinger.application.bioluminate.propfilter.ValueSelectionDialog: A SFilteredListWidget that allows the user to select certain values of a property for the criterion.
            • schrodinger.application.desmond.gui._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
              • schrodinger.application.desmond.gui.MdcAdvancedDialog: Advanced Options dialog for Mdc Desmond panels
              • schrodinger.application.desmond.gui.MinAdvancedDialog: Advanced Minimization options dialog for Desmond panels
          • PyQt4.QtGui.QDockWidget: QDockWidget(QString, QWidget parent=None, Qt.WindowFlags flags=0) QDockWidget(QWidget parent=None, Qt.WindowFlags flags=0)
            • schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget: The dock widget that can set a ViewerWindow as the main widget.
          • PyQt4.QtGui.QFrame: QFrame(QWidget parent=None, Qt.WindowFlags flags=0)
            • schrodinger.application.desmond.fep_gui.HorizontalBar
            • schrodinger.application.desmond.gui.HorizontalBar
            • schrodinger.ui.qt.appframework.JobInputFrame: An application input source selection widget.
            • PyQt4.QtGui.QAbstractScrollArea: QAbstractScrollArea(QWidget parent=None)
              • PyQt4.QtGui.QAbstractItemView: QAbstractItemView(QWidget parent=None)
                • PyQt4.QtGui.QListView: QListView(QWidget parent=None)
                  • PyQt4.QtGui.QListWidget: QListWidget(QWidget parent=None)
                    • schrodinger.ui.qt.swidgets.SListWidget: A QListWidget that can set its items and set up a callback at creation.
                      • schrodinger.ui.qt.swidgets.SFilteredListWidget: An SListWidget with an additional line edit that can be used to filter the items within the ListWidget
                        • schrodinger.application.bioluminate.propfilter.SelectingFilteredListWidget: A QListWidget that contains a edit to allow the user to filter the contents of the widget.
                • PyQt4.QtGui.QTableView: QTableView(QWidget parent=None)
                  • schrodinger.ui.qt.table.DataViewerTable
                    • schrodinger.ui.qt.table.SEasySDTable: A simple class that automatically sets up the table/model/delegate trio for a table object
                      • schrodinger.antibody_db_manage_gui.Editable: A table class that allows editing of cells
                  • PyQt4.QtGui.QTableWidget: QTableWidget(QWidget parent=None) QTableWidget(int, int, QWidget parent=None)
                    • schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable: Table that is used to show and carry out actions on all databases loaded by user.
              • PyQt4.QtGui.QGraphicsView: QGraphicsView(QWidget parent=None) QGraphicsView(QGraphicsScene, QWidget parent=None)
                • schrodinger.ui.sketcher.sketcherView
            • PyQt4.QtGui.QLabel: QLabel(QWidget parent=None, Qt.WindowFlags flags=0) QLabel(QString, QWidget parent=None, Qt.WindowFlags flags=0)
              • schrodinger.application.desmond.fep_gui.AdvLabel: A mutli-line label with small, bold text.
              • schrodinger.application.desmond.cwidget.AdvLabel: A mutli-line label with small, bold text.
              • schrodinger.application.bioluminate.pml_menus.ColorLabel: A label that shows off the color each element will be colored if this menu item is chosen.
              • schrodinger.application.desmond.cwidget.DesresTradeMark: Class for drawing the Desmond trademark logo to the GUI.
            • PyQt4.QtGui.QSplitter: QSplitter(QWidget parent=None) QSplitter(Qt.Orientation, QWidget parent=None)
              • schrodinger.ui.sequencealignment.sequence_viewer.SequenceViewer: The sequence viewer widget displays and manipulates sequences and associated data.
                • schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer: Creates a sequence viewer that can be opened by an action or added to a main window as a dockable item.
            • schrodinger.application.bioluminate.protein_report_widget.ReportFrame: A QtGui.QFrame that contains a Protein Report
              • schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart: A Protein Report widget that can deal with multiple protein structures and also has a slider chart that can be used to select residues.
            • schrodinger.application.bioluminate.pml_menus.ResultsWindow
            • schrodinger.application.bioluminate.sliderchart.SliderPlot: A chart that contains four lines the user can slide to select a region of the chart.
          • PyQt4.QtGui.QGroupBox: QGroupBox(QWidget parent=None) QGroupBox(QString, QWidget parent=None)
            • schrodinger.application.desmond.gui.AtomGroupFrame: Frame for the "Atom group" box of the Misc tab of the Advanced Options dialog.
            • schrodinger.application.desmond.gui.InputGroup: Group Frame for showing the widgets for loading the system model.
            • schrodinger.application.desmond.gui.MinOutputFrame: Group box "Output" of the "Minimization" tab of Advanced Options dialog.
            • schrodinger.application.desmond.gui.MinimizerFrame: Group box "Minimizer" of the "Minimization" tab of Advanced Options dialog.
            • schrodinger.application.desmond.gui.RandVelFrame: Frame for the "Randomize velocities" group of the Misc tab of Advanced dialog.
            • schrodinger.application.desmond.gui._BaseGroup: Enherited by MdGroup and MinimizeGroup, so therefore by all Simulation frames
              • schrodinger.application.desmond.gui.MdGroup: Molecular Dynamics group
            • schrodinger.application.desmond.fep_gui._ProtItem: Frame for each checkable group of the second tab of the panel (Plan Calculation).
            • schrodinger.application.desmond.cwidget._SdIncorpFrame: The incorporation (output) frame of the start dialog.
            • schrodinger.application.desmond.cwidget._SdJobFrame: Frame for the master job options
            • schrodinger.application.desmond.cwidget._SdMasterjob
            • schrodinger.application.desmond.cwidget._SdSubjobFrame
          • PyQt4.QtGui.QLineEdit: QLineEdit(QWidget parent=None) QLineEdit(QString, QWidget parent=None)
            • schrodinger.application.bioluminate.bwidgets.NumericLineEdit: A QtGui.QLineEdit with a builtin validator for floats or integers.
          • PyQt4.QtGui.QMainWindow: QMainWindow(QWidget parent=None, Qt.WindowFlags flags=0)
            • schrodinger.ui.qt.appframework.AppFramework: The AppFramework class is basically a hull for applications.
              • schrodinger.antibody_db_manage_gui.AdvancedOptionsPanel: The panel to change advanced options
              • schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog: A class which displays a dialog with a plot of the statistics for the most recent clustering
              • schrodinger.antibody_db_manage_gui.DBManagePanel: The Main Panel Class
              • schrodinger.application.canvas.clustergui.DendrogramPlotDialog: A class which displays a dialog with a plot of the dendrogram from the most recent clustering
              • schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog: A class which displays a dialog with a plot of the distance matrix associated with the most recent clustering
              • schrodinger.application.desmond.gui.GuiApp: Base class of several Desmond panel GUI's (see its subclasses below).
              • schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer: The Main Panel Class
              • schrodinger.ui.chooseligand.TestApp: Class for testing this module.
              • schrodinger.ui.qt.appframework.TestApp: Class for testing AppFramework outside of Maestro.
              • schrodinger.application.desmond.fep_gui._App: Class shared by Desmond and Mcpro applications
                • schrodinger.application.desmond.fep_gui.DesmondApp: Class shared by all Desmond panels.
                • schrodinger.application.desmond.fep_gui.McproApp: Class shared by all Mcpro panels
            • schrodinger.application.bioluminate.ssv.viewer.ViewerWindow: Provides the SimplifiedSequenceViewer with a window to occupy.
            • schrodinger.ui.sketcher.sketcher
          • PyQt4.QtGui.QMenu: QMenu(QWidget parent=None) QMenu(QString, QWidget parent=None)
            • schrodinger.application.bioluminate.pml_menus.ColorByElementSubMenu: The Color by Element submenu
            • schrodinger.application.bioluminate.pml_menus.PMLMenu: The base menu class we subclass from
              • schrodinger.application.bioluminate.pml_menus.ActionMenu: The Action menu
              • schrodinger.application.bioluminate.pml_menus.AroundExpandSubMenu: The modify-around submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.AsMenu: The Show->As submenu
              • schrodinger.application.bioluminate.pml_menus.AutoColorSubMenu: The Color menu
              • schrodinger.application.bioluminate.pml_menus.ColorChainSubMenu: The ColorChainSubMenu menu
              • schrodinger.application.bioluminate.pml_menus.ColorMenu: The Color menu
              • schrodinger.application.bioluminate.pml_menus.ColorSpectrumSubMenu: The ColorSpectrumSubMenu menu
              • schrodinger.application.bioluminate.pml_menus.ColorSubstructureSubMenu: The ColorSubstructureSubMenu menu
              • schrodinger.application.bioluminate.pml_menus.CompleteSubMenu: The modify-complete submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.ComputeSubMenu: The Action Compute submenu
              • schrodinger.application.bioluminate.pml_menus.EntrySubMenu: A submenu that lists all enabled Entry objects
              • schrodinger.application.bioluminate.pml_menus.ExcludeSubMenu: The modify-exclude submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.ExtendSubMenu: The modify-extend submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.FindPCSubMenu: The Find Polar Contacts submenu
              • schrodinger.application.bioluminate.pml_menus.GenSelectionSubMenu: The Action Generate Selection submenu
              • schrodinger.application.bioluminate.pml_menus.GenSymMatesSubMenu: The Action Generate Symmetry Mates submenu
              • schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu: The submenu that contains all the main actions used for most context menus
                • schrodinger.application.bioluminate.pml_menus.ObjectFreeContextSubMenu: The GeneralContextSubMenu for a right-click that is not on an object
                • schrodinger.application.bioluminate.pml_menus.SubstructureContextSubMenu: The GeneralContextSubMenu for a right-click that is on an atom
              • schrodinger.application.bioluminate.pml_menus.GenerateSubMenu: The Action Generate submenu
              • schrodinger.application.bioluminate.pml_menus.HideHydrogenSubMenu: The Hide Hydrogen submenu
              • schrodinger.application.bioluminate.pml_menus.HideMenu: The Hide menu
              • schrodinger.application.bioluminate.pml_menus.HydrogenSubMenu: The Action Hydrogen submenu
              • schrodinger.application.bioluminate.pml_menus.IncludeSubMenu: The modify-include submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.InvertSubMenu: The modify-invert submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.LabelAtomIdentSubMenu: The Label Atom Identifiers submenu
              • schrodinger.application.bioluminate.pml_menus.LabelMenu: The Label menu
              • schrodinger.application.bioluminate.pml_menus.LabelOtherSubMenu: The Label Other Properties submenu
              • schrodinger.application.bioluminate.pml_menus.LigandSitesSubMenu: The Action-Preset-Ligand Sites submenu
              • schrodinger.application.bioluminate.pml_menus.ModifySubMenu: The modify submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.PMLContextMenu: The base menu class we subclass from for context menus
                • schrodinger.application.bioluminate.pml_menus.AtomContextMenu: The context menu for right-clicks on non-selected atoms
                • schrodinger.application.bioluminate.pml_menus.SelectedAtomContextMenu: The context menu for right-clicks on selected atoms
                • schrodinger.application.bioluminate.pml_menus.SpaceContextMenu: The context menu for right-clicks in space
              • schrodinger.application.bioluminate.pml_menus.PolarContactsSubMenu: The Polar Contacts submenu
              • schrodinger.application.bioluminate.pml_menus.PresetSubMenu: The Preset submenu
              • schrodinger.application.bioluminate.pml_menus.RestrictSubMenu: The modify-restrict submenu of the action menu
              • schrodinger.application.bioluminate.pml_menus.SelectedAtomContextActionSubMenu: The submenu that allows the user to enable/disable individual objects
              • schrodinger.application.bioluminate.pml_menus.SelectionSubMenu: A submenu that lists all enabled Entry objects
              • schrodinger.application.bioluminate.pml_menus.ShowMenu: The Show menu
              • schrodinger.application.bioluminate.pml_menus.SurfaceAreaSubMenu: The Action Surface Area submenu
              • schrodinger.application.bioluminate.pml_menus.ToggleStateSubMenu: The submenu that allows the user to enable/disable individual objects
            • schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu: A submenu that shows the most recently chosen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
              • schrodinger.application.bioluminate.pml_menus.RecentCarbonColorSubMenu: A submenu that shows the most recently chosen carbon colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
              • schrodinger.application.bioluminate.pml_menus.RecentHydrogenColorSubMenu: A submenu that shows the most recently chosen hydrogen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
              • schrodinger.application.bioluminate.pml_menus.RecentObjectColorSubMenu: A submenu that shows the most recently chosen object colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
            • schrodinger.application.bioluminate.pml_menus.ShowOrganicMenu: The Show->Organic submenus
            • schrodinger.application.bioluminate.pml_menus.ShowSubstructureMenu: The Show->substructure submenus
          • PyQt4.QtGui.QProgressBar: QProgressBar(QWidget parent=None)
            • schrodinger.ui.qt.appframework.CustomProgressBar: Class for a custom progress bar (at the bottom of some panels).
          • PyQt4.QtGui.QToolBar: QToolBar(QString, QWidget parent=None) QToolBar(QWidget parent=None)
            • schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar: Get the toolbar that has the combobox with the antibody numering schemes.
            • schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar: A toolbar associated with the viewer that will handle display options.
            • schrodinger.application.bioluminate.ssv.toolbars.FindToolBar: Create an instance of the "Find Pattern" toolbar from the MSV.
            • schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar: Get the toolbar that has the import dialogs.
            • schrodinger.ui.sketcher.sketcherGUIMultiColumnToolBar
          • schrodinger.application.desmond.gui.RelaxFrame: Frame that includes the "Relax model..." check box and the relaxation protocol entry field.
          • schrodinger.application.desmond.gui.RestraintsTab: Frame for the Restraints tab of the Advanced Options dialog
          • schrodinger.application.bioluminate.bwidgets.RowActionItem: Custom widget to be used in a table cell.
          • schrodinger.application.desmond.gui.SimOptionsFrame: Responsible for drawing the simulation options widgets, including Simulation time and Recording intervals.
          • schrodinger.application.desmond.fep_gui._DesmondProt: Frame for the second tab ("Plan Calculation") of the Desmond GUIs.
          • schrodinger.ui.qt.appframework._EntryField: A special composite widget which contains a labeled line edit field.
          • schrodinger.application.desmond.fep_gui._LigMut: Class of the "Ligand Functional Group Mutation by FEP" panel.
          • schrodinger.application.desmond.fep_gui._McproProt: Frame for the second tab ("Plan Calculation") of the Mcpro GUIs.
          • schrodinger.application.desmond.fep_gui._Pert: Frame for the bottom part of the "Plan Calculation" tab of Mcpro GUIs.
          • schrodinger.application.desmond.fep_gui._ProMut: Main code of the Protein Residue Mutation GUI
          • schrodinger.application.desmond.fep_gui._RingMut
          • schrodinger.application.desmond.cwidget._SdDetailFrame: Frame for the section that gets shown when the "Detail" button is toggled on.
  • type: type(object) -> the object's type type(name, bases, dict) -> a new type
    • abc.ABCMeta: Metaclass for defining Abstract Base Classes (ABCs).
    • schrodinger.application.desmond.ffiostructure._FEPIOSubBlockMeta: A meta-class to different fepio sub block type classses.
    • schrodinger.application.desmond.ffiostructure._FFIOSubBlockMeta: A meta-class to different ffio sub block type classses.
    • schrodinger.application.desmond.picklejar.Picklable.__metaclass__
      • schrodinger.application.desmond.cmj.StageBase.__metaclass__
    • schrodinger.application.desmond.systype.TyperBase.__metaclass__
• schrodinger.application.mcpro.zmat.proteinHandler: Class provides methods to write the pepz input file
• schrodinger.ui.widget.pmwwidget.schroPmwWrapper: Parent class for all Schrodinger Pmw widgets.
  • schrodinger.ui.widget.pmwwidget.Balloon: Class that mimics the Pmw.Balloon class.
  • schrodinger.ui.widget.pmwwidget.ButtonBox: Class that mimics the Pmw.ButtonBox class.
  • schrodinger.ui.widget.pmwwidget.ComboBox: Class that mimics the Pmw.ComboBox class.
    • schrodinger.ui.propertyselector.PropertySelectorMenu: Pull-down menu style property selected Used by VSW GUI
    • schrodinger.application.desmond.table.TableComboBox._ComboBox
  • schrodinger.ui.widget.pmwwidget.Counter: Class that mimics the Pmw.Counter class.
  • schrodinger.ui.widget.pmwwidget.Dialog: Class that mimics the Pmw.Dialog class.
  • schrodinger.ui.widget.pmwwidget.EntryField: Class that mimics the Pmw.EntryField class.
    • schrodinger.ui.widgettable.EntryFieldCell: Subclass of Tkinter EntryField and Cell.
    • schrodinger.application.desmond.table.TableEntryField._EntryField
  • schrodinger.ui.widget.pmwwidget.Group: Class that mimics the Pmw.Group class.
  • schrodinger.ui.widget.pmwwidget.MainMenuBar: Class that mimics the Pmw.MainMenuBar class.
  • schrodinger.ui.widget.pmwwidget.MessageDialog: Class that mimics the Pmw.Dialog class.
    • schrodinger.ui.widget.pmwwidget.showinfo: Class designed to mimic the tkMessageBox.showinfo class with the caveat that a parent argument must be specified.
    • schrodinger.ui.widget.pmwwidget.showwarning: Class designed to mimic the tkMessageBox.showwarning class with the caveat that a parent argument must be specified.
  • schrodinger.ui.widget.pmwwidget.NoteBook: Class that mimics the Pmw.NoteBook class.
  • schrodinger.ui.widget.pmwwidget.OptionMenu: Class that mimics the Pmw.OptionMenu class.
    • schrodinger.ui.widgettable.OptionMenuCell: Subclass of Tkinter OptionMenu and Cell.
  • schrodinger.ui.widget.pmwwidget.PanedWidget: Class that mimics the Pmw.PanedWidget class.
  • schrodinger.ui.widget.pmwwidget.PromptDialog: Class that mimics the Pmw.Dialog class.
  • schrodinger.ui.widget.pmwwidget.RadioSelect: Class that mimics the Pmw.RadioSelect class.
  • schrodinger.ui.widget.pmwwidget.ScrolledCanvas: Class that mimics the Pmw.ScrolledCanvas class.
  • schrodinger.ui.widget.pmwwidget.ScrolledFrame: Class that mimics the Pmw.ScrolledFrame class.
    • schrodinger.application.desmond.table.Table: A table widget class.
  • schrodinger.ui.widget.pmwwidget.ScrolledListBox: Class that mimics the Pmw.ScrolledListBox class.
  • schrodinger.ui.widget.pmwwidget.ScrolledText: Class that mimics the Pmw.ScrolledText class.
• schrodinger.ui.widget.tkinterwidget.schroWidget: Class for all schrodinger Tkinter widgets.
  • schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
    • schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
  • schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
    • schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
  • schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
    • schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
  • schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
  • schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
    • schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
    • schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
    • schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
    • schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
      • schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
      • schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
    • schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
    • schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
    • schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
    • schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
    • schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
    • schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
    • schrodinger.application.desmond.table._TableWidget: A base class for all Table* widget classes except the Table class.
      • schrodinger.application.desmond.table.TableButton: Defines a button widget (similar to the Tkinter one) upon '_TableWidget'.
      • schrodinger.application.desmond.table.TableCheckbutton: Defines a check-button widget (similar to the Tkinter one) upon _TableWidget.
      • schrodinger.application.desmond.table.TableComboBox: Defines a ComboBox widget (similar to 'Pmw.ComboBox') upon _TableWidget.
      • schrodinger.application.desmond.table.TableEntry: Defines a entry widget (similar to the Tkinter one) upon '_TableWidget'.
      • schrodinger.application.desmond.table.TableEntryField: Defines a entry widget (similar to 'Pmw.EntryField') upon _TableWidget.
      • schrodinger.application.desmond.table.TableLabel: Defines a label widget (similar to the Tkinter one) upon '_TableWidget'.
      • schrodinger.application.desmond.table.TableRadiobutton: Defines a radio-button widget (similar to the Tkinter one) upon _TableWidget.
      • schrodinger.application.desmond.table.TableSpinbox: Defines a spin box widget (similar to the Tkinter one) upon '_TableWidget'.
      • schrodinger.application.desmond.table.TableTextButton: Defines a text-button widget upon '_TableWidget'.
      • schrodinger.application.desmond.table.TableTitle: Defines a Button widget (similar to the Tkinter one) upon '_TableWidget'.
  • schrodinger.ui.widget.tkinterwidget.HorizontalBar: Class intended to mimic the horizontal bar that divides the bottom buttons from the rest of the panel in Maestro.
  • schrodinger.ui.widget.tkinterwidget.Label: Class that mimics the Tkinter.Label class.
    • schrodinger.ui.widgettable.LabelCell: Subclass of Tkinter Label widget and Cell.
  • schrodinger.ui.widget.tkinterwidget.LabelFrame: Class that mimics the Tkinter.LabelFrame class.
  • schrodinger.ui.widget.tkinterwidget.Listbox: Class that mimics the Tkinter.Listbox class.
  • schrodinger.ui.widget.tkinterwidget.Menu: Class that mimics the Tkinter.Menu class.
  • schrodinger.ui.widget.tkinterwidget.Menubutton: Class that mimics the Tkinter.Menubutton class.
  • schrodinger.ui.widget.tkinterwidget.Message: Class that mimics the Tkinter.Message class.
  • schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
  • schrodinger.ui.widget.tkinterwidget.PanedWindow: Class that mimics the Tkinter.PanedWindow class.
  • schrodinger.ui.widget.tkinterwidget.PhotoImage: Class that mimics the Tkinter.PhotoImage class.
  • schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
    • schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
    • schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
  • schrodinger.ui.widget.tkinterwidget.Radiobutton: Class that mimics the Tkinter.Radiobutton class.
    • schrodinger.ui.widgettable.RadiobuttonCell: Subclass of Tkinter Radiobutton widget and Cell.
  • schrodinger.ui.widget.tkinterwidget.Scale: Class that mimics the Tkinter.Scale class.
  • schrodinger.ui.widget.tkinterwidget.Scrollbar: Class that mimics the Tkinter.Scrollbar class.
  • schrodinger.ui.widget.tkinterwidget.Spinbox: Class that mimics the Tkinter.Spinbox class.
    • schrodinger.application.desmond.table.TableSpinbox._Spinbox
  • schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
  • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
  • schrodinger.ui.widget.tkinterwidget.Toplevel: Class that mimics the Tkinter.Toplevel class.