Class Hierarchy

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• schrodinger.application.desmond.enhsamp.ASLObject
• urllib2.AbstractBasicAuthHandler
• urllib2.AbstractDigestAuthHandler
• 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.application.combiglide.packages.chutils.Adduct: An instance stores required information about an adduct molecule and supplies APIs for later retrieval.
• schrodinger.trajectory.analysistool.AnalysisTool: AnalysisTool is a base class for creating analyses of schrodinger.trajectory.desmondsimulation.DesmondSimulation objects.
• schrodinger.job.app.App: A class to handle all aspects of job setup and running.
• schrodinger.application.combiglide.packages.chutils.ApplyJoiningRules: APIs to determine what adduct rule matches are required for each substrate attachment point and what rule matches are exhibited for each adduct attachment point.
• schrodinger.structutils.analyze.AslLigandSearcher: Search a Structure instance for putative ligands with an Atom Selection Language expression.
• schrodinger.structutils.assignbondorders.AssignBondOrders
• schrodinger.application.desmond.gui.AtomGroupRow
• schrodinger.application.desmond.fep_mapping.AtomMappingData: Class to store intermediary and final data structures for atom mapping
• schrodinger.protein._reliability.Packing.AtomType: data structure to hold an atom type
• schrodinger.application.combiglide.packages.chutils.Attachment: Store information about an attachment point, which is a heavy atom on a structure.
• requests.auth.AuthBase
• schrodinger.pipeline.pipeutils.BackwardsReader: Read a file line by line, backwards.
• schrodinger.application.desmond.fepdiff.BaseBlockProperty
• urllib2.BaseHandler
• schrodinger.job.queue.BaseJob: A base job class for jobs run under JobDJ.
• SocketServer.BaseRequestHandler: Base class for request handler classes.
• SocketServer.BaseServer: Base class for server classes.
• schrodinger.structutils.sitealign.BindingSiteAligner: Align structures by matching binding site atoms.
• schrodinger.application.combiglide.packages.chutils.BitArray: Minimal bit-array class
• schrodinger.application.desmond.fepdiff.BlockDiffer
• 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.cns_io.CNSData
• schrodinger.application.desmond.meta.CV: base class for collective variable
• 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.combiglide.packages.chutils.ChUtils: Utilities generally useful in core-hopping
• schrodinger.infra.canvas2d.ChemViewAnnotator
• schrodinger.infra.canvas2d.ChemViewAnnotator
• schrodinger.application.canvas.utils.ChmCSVTools
• 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.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.ui.qt.appframework.ConfigDialog: Toplevel Qt widget that mimics the Maestro Start dialog.
• 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.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns: Constants for table columns.
• schrodinger.application.glide.glide.ConstraintGroup: Class defining a constraint group.
• schrodinger.application.desmond.mdpose.mdpose_analysis.ContactCmd
• schrodinger.application.combiglide.packages.core_classifier.CoreClassifier: Partition to generate structural partitions for a structure containing a single ring system.
• schrodinger.utils.ligfilter.Criterion: A base class for a structure matching criterion.
• 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.application.qsite.input.Cut: A class to handle representation and printing of general qm region cuts.
• schrodinger.application.canvas.r_group_dee.DEE_Backtracking
• schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix
• schrodinger.application.canvas.r_group.Data: Class to store intermediary and finals data structures for R-group analysis.
• schrodinger.ui.qt.utils.DefaultMessageDelegate
• schrodinger.ui.qt.utils.DefaultMessageDelegate
• 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
• csv.Dialect: Describe an Excel dialect.
  • csv.excel: Describe the usual properties of Excel-generated CSV files.
    • schrodinger.application.canvas.utils.chm_bluebird
    • schrodinger.application.canvas.utils.chm_excel
• schrodinger.ui.appframework.DialogParameters: Class for holding dialog parameters.
• UserDict.DictMixin
• schrodinger.application.jaguar.output.Dipole: A class for storing dipole information.
• schrodinger.structutils.measure.DistanceCellIterator: Iterate through neighbors of specified atoms.
• schrodinger.pipeline.stage.DotPrinter: Class for printing a progress period or percentage every N number of iterations.
• schrodinger.pipeline.pipeutils.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.application.desmond.fepdiff.DualIndexMapper
• schrodinger.project.EmptyIterator: Empty iterator.
• schrodinger.application.desmond.energygroup.EnergyComponent: Class for storing different energy components.
• schrodinger.application.desmond.energygroup.EnergyGroupAnalysis: General Energy Group analysis class.
• 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.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.prime.primefix.FixForPrime: Wrapper class to house the combination of methods for fixing a structure for Prime.
• schrodinger.protein._reliability.Packing.FragBox: data structure to hold a fragment in a 'box'
• schrodinger.application.desmond.fep_gui.FragClass: Class for storing the data for each fragment row.
• schrodinger.protein._reliability.Packing.Fragment: data structure to hold a fragment type
• 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.jaguar.output.FukuiIndices: A class to store Atomic Fukui indices.
• schrodinger.application.desmond.gaussian_filter.GaussianFilter
• pyevolve.GenomeBase.GenomeBase
• 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.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
      • 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.
    • Tkinter.Text: Text widget which can display text in various forms.
      • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
• 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.application.jaguar.make_headers_mod.HeaderWriter: Class to write a file structured as a header with sections for integer, real and string, etc keywords followed by a footer.
• 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.
• schrodinger.application.combiglide.packages.hierarchy.Hierarchy: Class that stores the structure of the hierarchy.
• schrodinger.application.qsite.input.HydrogenCap: A class to handle representation and printing of hydrogen caps for the qm region.
• 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.desmond.fepdiff.IndexMapper
• schrodinger.application.jaguar.output.JaguarAtomicResults: A class for holding atomic level properties.
• schrodinger.application.jaguar.output.JaguarOptions: A class for keeping track of specific calculation options.
• schrodinger.application.jaguar.output.JaguarOutput
• schrodinger.application.jaguar.output.JaguarResults: A class for holding results for a specific geometry.
• schrodinger.application.jaguar.make_headers_mod.JaguarTemplates: Class containing text block templates for Jaguar auto-generated C-style header files.
• schrodinger.job.queue.JobDJ: Class for running commands/jobs in parallel under jobcontrol.
• schrodinger.ui.appframework.JobParameters: Class for holding job parameters.
• schrodinger.application.combiglide.packages.chutils.Join: An object is an allowed join between an attachment atom on a Substrate object and an attachment atom on an Adduct object.
• schrodinger.application.combiglide.packages.chutils.JoiningRules: Store joining rules read from a file and provide access methods.
• schrodinger.protein._reliability.Lattice: Class to more conveniently contain space group and unit cell information extracted from a structure.Structure.
• schrodinger.job.launcher.Launcher: Run a program (typically a Python or shell script) under job control.
• schrodinger.structutils.analyze.Ligand: A putative AslLigandSearcher ligand structure with read-only data and convenience methods.
• schrodinger.job.queue.LinkedList: A doubly linked list, providing constant time addition, size, and truth checks.
• 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.application.desmond.mdpose.mdpose_analysis.MDPoseAnalysis
• schrodinger.application.desmond.mdpose.mdposejob.MDSimulation
• schrodinger.application.combiglide.packages.chutils.MakeRLinkerUtils: Utility functions for use with make_r_linker_sqlite().
• schrodinger.utils.pymol.Mapping: Mappings from Maestro codes to PyMOL representations and settings
• _Pmw.Pmw_1_3.lib.PmwBase.MegaArchetype
  • _Pmw.Pmw_1_3.lib.PmwMainMenuBar.MainMenuBar
    • schrodinger.ui.widget.pmwwidget.MainMenuBar: Class that mimics the Pmw.MainMenuBar class.
  • _Pmw.Pmw_1_3.lib.PmwBase.MegaToplevel
    • _Pmw.Pmw_1_3.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_3.lib.PmwBase.MegaWidget
    • _Pmw.Pmw_1_3.lib.PmwButtonBox.ButtonBox
      • schrodinger.ui.widget.pmwwidget.ButtonBox: Class that mimics the Pmw.ButtonBox class.
    • _Pmw.Pmw_1_3.lib.PmwGroup.Group
      • schrodinger.ui.widget.pmwwidget.Group: Class that mimics the Pmw.Group class.
    • _Pmw.Pmw_1_3.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_3.lib.PmwRadioSelect.RadioSelect
      • schrodinger.ui.widget.pmwwidget.RadioSelect: Class that mimics the Pmw.RadioSelect class.
    • _Pmw.Pmw_1_3.lib.PmwScrolledCanvas.ScrolledCanvas
      • schrodinger.ui.widget.pmwwidget.ScrolledCanvas: Class that mimics the Pmw.ScrolledCanvas class.
    • _Pmw.Pmw_1_3.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.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.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.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.
• schrodinger.structutils.minimize.Minimizer: A class to provide force field energy and minimization.
• 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.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
        • 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.
      • Tkinter.Text: Text widget which can display text in various forms.
        • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
  • Tkinter.Tk: Toplevel widget of Tk which represents mostly the main window of an application.
    • schrodinger.ui.widget.tkinterwidget.Tk: This is a Schrodinger-ized Tk instance.
• schrodinger.trajectory.rmsd2d.ModelBase
• schrodinger.protein._reliability.ModelCheck
• 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.application.jaguar.make_headers_mod.MopacTemplates: Class containing text block templates for MOPAC auto-generated C-style header files.
• 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.
• collections.MutableMapping
• 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.
• schrodinger.application.jaguar.output.NormalMode
• 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.
• schrodinger.application.jaguar.output.Orbital: A class for storing orbital information.
• schrodinger.trajectory.pbc_manager.PBCMeasureMananger: A class to measure distance, angle, dihedral and planar angle under periodic boundary conditions.
• 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.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
      • 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.
    • Tkinter.Text: Text widget which can display text in various forms.
      • schrodinger.ui.widget.tkinterwidget.Text: Class that mimics the Tkinter.Text class.
• schrodinger.protein._reliability.Packing: read in parameters for packing calculation report residue Z-score
• schrodinger.application.desmond.energygroup.PairDict: PairDict is a special dictionary that treats pairs with the same element as equals, independent of order.
• schrodinger.application.combiglide.packages.hierarchy.Partition: A Partition in the hierarchy.
• schrodinger.application.combiglide.packages.hierarchy.Partitioning: A partitioning in the hierarchy.
• 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.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.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
      • 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.
    • 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.gui.PosResRow
• schrodinger.application.glide.glideanalysis.PoseLibrary: A helper class to sort a pose library.
• schrodinger.application.bioluminate.protein.PrimeStructure
• schrodinger.job.queue.PriorityQueue: This is a general priority queue.
• multiprocessing.Process
• 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.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.
• PyQt4.QtCore.QAbstractListModel
• PyQt4.QtCore.QAbstractListModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtCore.QAbstractTableModel
• PyQt4.QtGui.QAction
• PyQt4.QtGui.QCheckBox
• PyQt4.QtGui.QCheckBox
• PyQt4.QtGui.QCheckBox
• PyQt4.QtGui.QComboBox
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDialog
• PyQt4.QtGui.QDockWidget
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QFrame
• PyQt4.QtGui.QGraphicsItem
• PyQt4.QtGui.QGraphicsItem
• PyQt4.QtGui.QGraphicsView
• PyQt4.QtGui.QGraphicsView
• PyQt4.QtGui.QGroupBox
• PyQt4.QtGui.QGroupBox
• PyQt4.QtGui.QGroupBox
• PyQt4.QtGui.QGroupBox
• PyQt4.QtGui.QGroupBox
• PyQt4.QtGui.QIcon
• PyQt4.QtGui.QIntValidator
• PyQt4.QtGui.QItemDelegate
• PyQt4.QtGui.QItemDelegate
• PyQt4.QtGui.QItemDelegate
• PyQt4.QtGui.QItemDelegate
• PyQt4.QtGui.QItemDelegate
• PyQt4.QtGui.QLabel
• PyQt4.QtGui.QLabel
• PyQt4.QtGui.QLabel
• PyQt4.QtGui.QLineEdit
• PyQt4.QtGui.QLineEdit
• schrodinger.application.qsite.input.QMRegion: A class to provide access to a &qmregion specification and the ability to create one on the fly.
• PyQt4.QtGui.QMainWindow
• PyQt4.QtGui.QMainWindow
• PyQt4.QtGui.QMenu
• PyQt4.QtGui.QMenu
• PyQt4.QtGui.QMenu
• PyQt4.QtGui.QMenu
• PyQt4.QtGui.QMenu
• PyQt4.QtGui.QMovie
• PyQt4.QtCore.QObject
• PyQt4.QtCore.QObject
• PyQt4.QtCore.QObject
• PyQt4.QtCore.QObject
• PyQt4.QtCore.QObject
• PyQt4.QtCore.QObject
• PyQt4.QtGui.QPushButton
• PyQt4.QtGui.QPushButton
• PyQt4.QtGui.QScrollArea
• schrodinger.application.qsite.input.QSiteInput
• PyQt4.QtGui.QSortFilterProxyModel
• PyQt4.QtGui.QSortFilterProxyModel
• PyQt4.QtGui.QSortFilterProxyModel
• PyQt4.QtGui.QSpinBox
• PyQt4.QtGui.QStyledItemDelegate
• PyQt4.QtGui.QStyledItemDelegate
• PyQt4.QtGui.QTableView
• PyQt4.QtGui.QTableWidget
• PyQt4.QtGui.QTableWidget
• PyQt4.QtGui.QTableWidget
• PyQt4.QtCore.QThread
• PyQt4.QtGui.QToolBar
• PyQt4.QtGui.QToolBar
• PyQt4.QtGui.QToolBar
• PyQt4.QtGui.QToolBar
• PyQt4.QtGui.QToolButton
• PyQt4.QtGui.QValidator
• PyQt4.QtGui.QValidator
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidget
• PyQt4.QtGui.QWidgetAction
• schrodinger.application.canvas.r_group.RGroupFinder: This class is used to find optimal core alignments and determines r-groups for input structures.
• schrodinger.trajectory.rmsd2d.RMSDCalculator: A multi-threading class to calculat pairwise RMSD on a set of trajectory frames.
• schrodinger.ui.qt.rama.Rama: A class showing a matplotlib plot of the Phi and Psi angles in a helix
• schrodinger.ui.rama.Rama
• schrodinger.ui.appframework.ReadDialog: Dialog allowing user to specify a file to read in.
• schrodinger.protein._reliability.RealSpaceFit
• 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.protein.analysis.Report: A class to calculate properties of proteins.
• schrodinger.application.report2d.Report2D
• schrodinger.job.queue.RequirementsJob: This is a base class that indicates a job has special requirements (e.g.
• schrodinger.protein._reliability.Packing.ResStats
• schrodinger.application.mcpro.residuetools.ResidueTools: Class with tools to help in manipulating proteins
• schrodinger.application.desmond.rest_inp.RestInput
• schrodinger.infra.mmcheck.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.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns: Constants for the full (i.e.
• schrodinger.application.jaguar.output.ScfIteration: A simple storage class for storing info on an SCF iteration.
• schrodinger.application.canvas.r_group_dee.SimulatedAnnealing
• 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.structure.SmilesStructure: SMILES representation of a Structure that is returned by SmilesReader and SmilesCsvReader.
• 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.analysis.enrichment.StatisticalSummary: Container class to store summary metrics describing an array of numerical values.
• schrodinger.application.report2d.StructInfo: Stores information that is needed to draw a structure to PDF/HTML.
• schrodinger.structure.Structure: A general chemical structure object, which may contain multiple molecules.
• 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.combiglide.packages.chutils.Substrate: An instance stores required information about a substrate molecule and supplies APIs for later retrieval.
• schrodinger.trajectory.analysis.Superimposer
• 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.application.canvas.r_group.TempAtom
• unittest.TestCase
• unittest.TestCase
• unittest.TestCase
• unittest.TestCase
• schrodinger.application.jaguar.output.TextParser: A parser to create a JaguarOutput object from a Jaguar output file.
• 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.trajectory.Torsion.Torsion: A class to contain the atom numbers for each torsion
• schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer: Summarize the similarity differences within and between two groups of fingerprints.
• UserDict.UserDict
• 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 application.
    • schrodinger.ui.widget.tkinterwidget.Tk: This is a Schrodinger-ized Tk instance.
  • Tkinter.Toplevel: Toplevel widget, e.g.
    • schrodinger.ui.widget.tkinterwidget.Toplevel: Class that mimics the Tkinter.Toplevel class.
• 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.
  • 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.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
• schrodinger.application.desmond.xvfbwrapper.Xvfb
• 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.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.structure._AtomBondContainer: The class to provide access to _StructureBond instances for each bond of an atom.
• schrodinger.structure._AtomCollection: A set of atoms, usually comprising a subset of the total atoms in a Structure.
• 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.infra.mmcheck._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.application.prepwizard._CommonProblemsFixer: Class for fixing common structure problems.
• schrodinger.trajectory.desmondsimulation._DesmondFrame: _DesmondFrame contains simulation data at a particular time.
• schrodinger.structutils.measure._DistanceCell
• schrodinger.application.desmond.ffiostructure._Element
• schrodinger.test.stu.outcomes.desmond_workups._EneFile: Class to find and contain the information in a Desmond .ene file.
• schrodinger.project._EntryGroupIterator: Iterator for entry groups in the project
• schrodinger.project._EntrySurfaceIterator: An iterator for the surfaces associated with a given entry.
• 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._FEPIOSubBlockContainer
• schrodinger.trajectory.ffstructure._FFAngleIterator
• schrodinger.trajectory.ffstructure._FFBondIterator
• schrodinger.trajectory.ffstructure._FFConstraintIterator
• schrodinger.trajectory.ffstructure._FFDihedralIterator
• schrodinger.trajectory.ffstructure._FFExclusionIterator
• 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._FFIOSubBlockContainer
• 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.maestro.maestro._IgnoreCallback: This is a context manager to ignore maestro callbacks inside a with: block
• schrodinger.project._IncludedRowsIterator: Iterator for included rows of the project or group
• 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.job.queue._MultiJobFinalizer: A class to allow specification of a function to be invoked when the final job of a group completes successfully.
• schrodinger.utils.ligfilter._MySplit
• schrodinger.application.desmond.ffiostructure._OtherBlock
• schrodinger.application.desmond.ffiostructure._OtherBlockContainer: The class to provide access to other block instances.
• reportlab.pdfgen.textobject._PDFColorSetter: Abstracts the color setting operations; used in Canvas and Textobject asseumes we have a _code object
• schrodinger.application.combiglide.packages.chutils._ParseRulesFile: Utility functions (no objects) to read and parse joining-rules files and to write new such files with proper syntax.
• schrodinger.test.stu.outcomes.standard_workups._PropertyCompare: Compare properties between a ct and a csv file generated from a ct via proplister.
• schrodinger.trajectory.analysis._RamachandranCallback: This class implements a callback to print information about selected Ramachandran plot points.
• schrodinger.structure._ResidueIterator: Residue iterator.
• schrodinger.structure._RingEdgeIterator: Iterates over edges(bonds) of a _Ring.
• schrodinger.project._SelectedRowsIterator: Iterator for selected rows of the project or group
• schrodinger.structure._StructureAtom: Access of mmct atoms properties pythonically.
• 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: 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.
• schrodinger.infra.mmcheck._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.application.combiglide.combenumdock._fakeEvent
• schrodinger.infra.mmreflect._object
• schrodinger.infra.mmsurf._object
• schrodinger.infra.mmgpgpu._object
• schrodinger.ui.qt.rama.Rama.backbone_dihedral
• schrodinger.ui.rama.Rama.backbone_dihedral
• 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.application.glide.liaison_lsbd.liaison
• schrodinger.application.jaguar.output.line_enumerate: A simple wrapper class to keep track of the line iteration count.
• 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.application.matsci.enumeration.Alchemist: Class that mutates the element of an atom in a structure
  • schrodinger.application.desmond.title_to_hex.Analysis
  • schrodinger.application.desmond.simulation_block_data.Array_Prop
  • schrodinger.application.desmond.cmj.AslValidator
  • schrodinger.application.desmond.cms.AtomGroup
  • schrodinger.application.desmond.mdkey.AtomGroup
  • schrodinger.application.desmond.gui.AtomGroupFrame: Frame for the "Atom group" box of the Misc tab of the Advanced Options dialog.
  • schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin: A mixin that automatically generates the jobname using the current panel settings.
  • 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.test.stu.client.ClientError: Generic STU client error.
      • schrodinger.application.desmond.systype.DetectionError
      • schrodinger.application.desmond.systype.FormatError
      • httplib.HTTPException
      • schrodinger.application.jaguar.make_headers_mod.IfTestError
      • schrodinger.application.licensing.flexlm.IncompatibleLicenseError: This exception is thrown from the merge operations when incompatibilities between the old and new license prevent make merging them impossible.
      • schrodinger.application.matsci.jaguarworkflows.JaguarFailedException: An exception that is thrown when either reading the Jaguar output file fails for some reason, or a successful reading shows that Jaguar failed.
      • schrodinger.application.jaguar.validation.JaguarKeywordException: Base exception class for all custom Jaguar keyword validation errors
      • schrodinger.application.jaguar.output.JaguarParseError
      • schrodinger.application.jaguar.gui.utils.JaguarSettingError: An exception indicating that there was an error with the user-specified Jaguar settings
      • schrodinger.job.jobcontrol.JobcontrolException
      • schrodinger.application.licensing.licerror.LicenseException: A LicenseException delivers a LicenseError up the call chain.
      • schrodinger.application.licensing.flexlm.LicfileError: This exception is thrown by the main code if asked to work with something that isn't an actual license file.
      • schrodinger.maestro.maestro.MaestroCommand: Raises an Exception and is used whenever a command fails to execute.
      • schrodinger.infra.mmcheck.MmException: An exception class that specifically indicates the failure of an mmlibs call.
      • schrodinger.application.mopac.results2012.MopacBasisError1
      • schrodinger.application.mopac.results2012.MopacBasisError2
      • schrodinger.application.mopac.results2012.MopacBasisError3
      • schrodinger.application.mopac.results2012.MopacBasisError4
      • schrodinger.application.mopac.results2012.MopacBasisError5
      • schrodinger.application.mopac.mopac_launchers.MopacLicenseError
      • schrodinger.application.mopac.results2012.MopacNumericalError
      • schrodinger.application.mopac.results2012.MopacPropertyError
      • schrodinger.application.mopac.mopac_launchers.MopacRuntimeError
      • schrodinger.maestro.markers.NotInWorkspaceError: An exception when trying to display a marker covering atoms that are not currently in the workspace.
      • schrodinger.structure.OptionError: A parent exception class to indicate an error in setting an option.
      • schrodinger.application.desmond.cmj.ParseError
      • schrodinger.utils.urllib.PasswordRetryException
      • schrodinger.infra.phase.PhpException: Proxy of C++ PhpException class
      • schrodinger.project.ProjectException
      • schrodinger.application.bioluminate.protein.PropkaError: A custom exception for any propka failures
      • schrodinger.trajectory.rdf.RDFException
      • schrodinger.application.canvas.r_group.RGroupException: This is a special exception, which is thrown when for some reason r-group calculation can not be completed.
      • 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.
        • exceptions.AssertionError: Assertion failed.
        • schrodinger.job.remote_command.CommandError: Used to report external commands that fail.
        • exceptions.ImportError: Import can't find module, or can't find name in module.
          • schrodinger.MaestroNotAvailableError: Error class to indicate that Maestro is not available and there was an attempt to use it.
        • exceptions.RuntimeError: Unspecified run-time error.
          • schrodinger.application.jaguar.output.IncompleteOutput: Indicators that the output is incomplete.
          • schrodinger.test.stu.run.JobDJError
          • 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
        • exceptions.TypeError: Inappropriate argument type.
          • schrodinger.job.hunt_stub.UsageError: Used to report illegal hunt options, or invalid combinations of options.
        • exceptions.ValueError: Inappropriate argument value (of correct type).
          • schrodinger.test.stu.client.ClientValueError: Arguments to a client function are incorrect, or not fully determined.
          • schrodinger.test.stu.testscripts.READMESyntaxError: Exception for issues with the syntax of a README file.
      • schrodinger.application.desmond.cmj.StopRequest
      • schrodinger.application.mopac.structure_launchers.StructureLauncherError
      • schrodinger.application.ligprep.ionizer.TolerableError: Raised when the structure could not be processed due to a non-fatal error.
      • schrodinger.application.ligprep.ionizer.TooManyGroupsError: Raised when the structure could not be processed because it has too many ionizable groups.
      • schrodinger.application.moldescriptors.TopoException
      • schrodinger.application.desmond.systype.UnknownAppError
      • schrodinger.application.desmond.systype.UnknownRuleError
      • schrodinger.test.stu.sysinfo.UnrecognizedPlatform: An unrecognized platform was found.
      • schrodinger.test.darwinconsole.UnsupportedPlatformException
      • schrodinger.application.licensing.licadmin.UsageError: This exception is thrown when unrecognized ior incompatible commandline options are used.
      • schrodinger.analysis.visanalysis.vdexception.VDException: This is a simple Exception derived class used by the various VolumeData associated components to denote an error condition.
      • exceptions.Warning: Base class for warning categories.
        • exceptions.UserWarning: Base class for warnings generated by user code.
      • schrodinger.test.stu.common.ZipError: Error while zipping up files.
  • 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.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns
  • schrodinger.application.desmond.simulation_block_test.Block
  • schrodinger.trajectory.BondRotator.BondRotator: perform RB scan
  • schrodinger.application.matsci.amorphous.Box: Class that defines the region a new structure may be placed in
  • schrodinger.application.matsci.amorphous.BuilderWithClashDetection: The base class for the amorphous builder classes
  • schrodinger.application.desmond.envir.CONST
  • schrodinger.analysis.enrichment.Calculator: A class to calculate enrichment terms for a screen.
  • 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.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.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.desmond.mdkey.CfgAtom: This class represents the "atomic" parameters in a config file.
  • schrodinger.protein.getpdb_utility.Chain: Class to handle splitting a chain out of a PDB file.
  • schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition: Manage a reaction channel definition.
  • schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions: Manage a collection of reaction channel definitions.
  • schrodinger.application.matsci.rxn_channel.rxn_channel.Channels: Manage the enumeration of reaction channels.
  • schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns
  • schrodinger.application.matsci.nano.slab.CheckInput: Manage checking user input.
  • schrodinger.application.matsci.rxn_path.CheckInput: Check user input.
  • schrodinger.application.matsci.nano.check.CheckInput: Check user input.
  • schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput: Manage checking user input.
  • schrodinger.application.matsci.nano.particle.CheckInput: Manage checking user input.
  • schrodinger.application.matsci.nano.xtal.CheckInput: Check user input.
  • schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput: Manage checking user input.
  • schrodinger.infra.canvas.ChmMol: Proxy of C++ ChmMol class
    • schrodinger.application.canvas.base.ChmMolPtr
  • schrodinger.infra.canvas.ChmRangeUIDFilter: Proxy of C++ ChmRangeUIDFilter class
    • schrodinger.infra.canvas.ChmColumnUIDFilter: Proxy of C++ ChmColumnUIDFilter class
      • schrodinger.application.canvas.base.ChmColumnUIDFilterPtr
    • schrodinger.infra.canvas.ChmRowUIDFilter: Proxy of C++ ChmRowUIDFilter class
      • schrodinger.application.canvas.base.ChmRowUIDFilterPtr
  • schrodinger.application.mopac.mopac_api.CmdlineParser
  • schrodinger.protein.getpdb_utility.Code: Class to handle all the various files for each PDB code.
  • schrodinger.structutils.color.Color: Represent a color as either an integer (colormap index) or a string (color name).
  • schrodinger.structutils.color.ColorRamp: An object for calculating colors on a customizable color ramp.
  • schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin
  • schrodinger.utils.colorscheme.ColorSchemeManager
  • schrodinger.application.jaguar.gui.tabs.base_tab.CombinedUi: An object that provides access to widgets across multiple ui files
  • schrodinger.application.matsci.buildcomplex.ComplexBuilder: A class used to build an organometallic complex
  • schrodinger.application.matsci.rxn_channel.rxn_channel.Constants: Manage some constants.
  • schrodinger.application.matsci.nano.constants.Constants: Collect constants.
  • schrodinger.application.desmond.cms.Constraint
  • schrodinger.application.matsci.shapes.ConvexPolyhedron: Class to manage a convex polyhedron.
  • schrodinger.application.matsci.rxn_path.Coord: Manage the properties of an internal coordinate.
  • schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateData: This class is a base class for constraint and scan coordinate classes.
  • 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.matsci.nano.xtal.Crystal: Main class for generating crystals.
  • schrodinger.application.matsci.nano.plane.CrystalPlane: Manage a crystal plane object.
  • schrodinger.application.matsci.nano.xtal.CrystalSystems: Manage the properties of the seven crystal systems.
  • schrodinger.application.matsci.nano.xtal.CrystalSystems.Cubic: Manage the cubic system.
  • schrodinger.application.matsci.shapes.Cylinder: Class to manage a cylinder.
  • 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.analysis.visanalysis.volumedatautils.DataPointLocator: The DataPointLocator class is a simple utility class that allows data-points that are 'close' to a given position in space to be located easily.
  • 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.infra.util.DecoratorAndContextManager: An abstract base class for context managers that can also be used to decorate functions and classes.
    • schrodinger.test.decorate_fflag.enable_feature_flag: Provides a decorator/context manager for enabling feature flags.
      • schrodinger.test.decorate_fflag.disable_feature_flag: Disable a feature flag as either a context manager or a decorator for a unittest.TestCase or a test function.
    • schrodinger.utils.env.swap_ld_library_path: Restore LD_LIBRARY_PATH to the value that it was when we first ran a toplevel script.
  • schrodinger.application.desmond.fepana.DeltaEnergy
  • schrodinger.application.desmond.fepdiff.DictDiffer: Calculate the difference between two dictionaries as: (1) items added (2) items removed (3) keys same in both but changed values (4) keys same in both and unchanged values
  • schrodinger.application.matsci.shapes.Edge: Class to manage edges.
  • schrodinger.ui.qt.swidgets.EnforcingValidatorMixin: This is a mixin class to be added to a QValidator subclass.
  • schrodinger.application.desmond.cmj.Engine
  • schrodinger.trajectory.prody.ensemble.Ensemble: A class for analysis of arbitrary conformational ensembles.
  • 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.desmond.gui.EnsembleClassFrame: Frame that includes the Ensemble class pull-down menu and the entry fields correspondint to it.
  • 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.project.EntryGroup: A class which represents 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.job.host_check.Error: An Error represents an system-level issue that prevents remote commands executed via ssh from succeeding.
  • schrodinger.infra.mmerr.ErrorHandler: A class for managing mmerr handlers.
  • schrodinger.infra.exception_handler.ExceptionRecorder: A top level exception handler that writes uncaught exceptions to a folder in .schrodinger.
  • schrodinger.application.desmond.fep_edge_data.FEPEdgeData: FEPEdgeData contains all the data related to an FEP perturbation.
  • schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker
  • schrodinger.application.desmond.replica_sid_generator.FEPReport
  • schrodinger.application.desmond.fep_reporter.FEPReportMaker
  • schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper: This is a mapper class used by FEP Scholar GUI so that we don't need to use Canvas MCS for matching molecule atoms.
  • schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator: This class generates master msj file that manages both solvent and complex legs of the FEP simulation.
  • schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport
  • schrodinger.application.matsci.shapes.Face: Class to manage faces.
  • schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro
  • schrodinger.application.glide.glide.FeaturePattern: Class defining a constraint feature pattern.
  • schrodinger.application.desmond.mdkey.FepSchedule
  • logging.Formatter: Formatter instances are used to convert a LogRecord to text.
  • schrodinger.application.ligprep.ionizer.Fragment: Class representing a fragment from the ionizer library.
  • schrodinger.structutils.createfragments.FragmentCreator: This class will break up input structures into fragments based on some simple rules.
  • schrodinger.application.bioluminate.antibody_utils.FrameworkTemplate
  • schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate
  • schrodinger.application.desmond.fepana.FreeEnergyContrib
  • schrodinger.application.bioluminate.antibody.search_results_table.FullColumns: Constants for the full (i.e.
  • 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.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization: Manage the genetic optimization.
  • schrodinger.application.matsci.textlogger.GetLogger: Set up a textwrapped log file.
  • schrodinger.application.glide.gui.GlideWorkspaceMarkers: Class for marking constraints and excluded volumes in the Workspace.
  • schrodinger.trajectory.analysis.Grid3D: A class for representing a function of 3D Cartesian coordinates discretize onto a grid.
  • schrodinger.graphics3d.gridbox.GridBox: Class for drawing a grid box to the Workspace.
  • schrodinger.graphics3d.common.Group: Class to group a bunch of primitives and draw them out.
  • schrodinger.application.matsci.nano.sheet.Grow: Manage the details of how to attach cells to the lattice of the desired shape.
  • schrodinger.application.glide.http_client.HTTPClient
  • schrodinger.application.desmond.starter.ui.multisim.Help
  • schrodinger.application.desmond.multisimstartup.Help
  • schrodinger.application.desmond.config._FepSchedule.Helper
  • schrodinger.application.matsci.nano.xtal.CrystalSystems.Hexagonal: Manage the hexagonal system.
  • schrodinger.application.matsci.nano.sheet.HoneycombBilayers: Create honeycomb bilayers.
  • schrodinger.application.matsci.nano.sheet.HoneycombCell: Manage cells in the honeycomb lattice.
  • schrodinger.application.matsci.nano.sheet.HoneycombLattice: Create the honeycomb lattice according to the following coordinate system:
  • schrodinger.application.matsci.nano.sheet.HoneycombUnitCell: Create a unit cell of a honeycomb lattice.
  • schrodinger.job.jobcontrol.Host: A class to encapsulate host info from the schrodinger.hosts file.
  • schrodinger.job.hunt_stub.HostEntry: HostEntry objects represent individual host entries in a 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.job.hunt_stub.HuntOptions: A class representing the settings that govern a 'unt' search.
  • schrodinger.application.phase.hypothesis.Hypothesis
  • schrodinger.test.ioredirect.IORedirect: Use to redirect stderr & stdout.
    • schrodinger.test.ioredirect.IOCapture: Use to redirect stderr & stdout to a StringIO object.
  • schrodinger.test.ioredirect.IOSilence: A context manager for doing a "deep suppression" of stdout and stderr, which will point the file descriptors to devnull.
    • schrodinger.test.ioredirect.FullIORedirect: Context manager returns an IOString with all output from stderr/stdout.
  • schrodinger.maestro.markers.Icons: Constants for marker icons
  • 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.application.jaguar.gui.input_tab_widgets.InputEntriesColumns: Column constants for the selected entries table
  • schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB: Column constants for the HB input tab entries table.
  • schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka: Column constants for the pKa selected entries table
  • schrodinger.application.desmond.gui.InputGroup: Group Frame for showing the widgets for loading the system model.
  • schrodinger.application.jaguar.gui.base_panel.InputMultiplicityMixin: Base class for any mixin that needs to get list of entries with spin multiplicities greater than one.
  • schrodinger.application.jaguar.gui.base_panel.InputTabMixin: A mixin for panels that use the Input tab.
  • 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.prime.residue_interaction.InteractionReader: Read the Prime residue interaction data from a structure
  • schrodinger.application.matsci.nano.interface_mod.Interface: Manage the building of an interface model.
  • schrodinger.application.bioluminate.pml_menus.InterfaceMixin: Determine the Protein-Protein interface atoms
  • schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces: Manage the enumeration of interfaces.
  • schrodinger.application.matsci.rxn_path.InternalCoords: Manage the internal coordinates of a structure.
  • schrodinger.application.ligprep.ionizer.Ionizer: Class for ionizing structures (part of LigPrep).
  • schrodinger.application.jaguar.input.JaguarInput: A class for specifying Jaguar input.
  • schrodinger.application.desmond.cmj.Job
  • schrodinger.job.jobcontrol.Job: A class to access a specific record in the job database.
  • schrodinger.application.desmond.cmj.JobErrorHandler
  • 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.application.desmond.cmj.JobOutput
  • schrodinger.application.desmond.cmj.JobStatus
  • schrodinger.application.desmond.mdkey.Key
  • schrodinger.application.jaguar.keywordDB.Keyword: A class to hold keyword info.
  • schrodinger.application.desmond.feputils.LabelSpinner: This object replaces a label's icon with a spinning progress icon when start() is called.
  • schrodinger.infra.licensing.License
  • schrodinger.utils.license.License: Class to allow easy licensing of Python scripts
  • schrodinger.application.licensing.flexlm.License: A License object represents a single FLEXlm license file.
  • schrodinger.application.licensing.licerror.LicenseError: A LicenseError represents a license-related error.
  • schrodinger.application.licensing.licadmin.LicenseFeature: A LicenseFeature object represents a particular license feature provided by a LicenseResource.
  • schrodinger.application.licensing.flexlm.LicenseLine: A LicenseLine object represents a single line of a FLEXlm license file.
    • schrodinger.application.licensing.flexlm.Feature: Feature objects represent FEATURE or INCREMENT lines in the license file.
    • schrodinger.application.licensing.flexlm.Package: A Package object represents a single PACKAGE line in the license file.
    • schrodinger.application.licensing.flexlm.Server: Server objects represent SERVER lines in the license file.
    • schrodinger.application.licensing.flexlm.UseServer: UseServer objects represent USE_SERVER lines in the license file.
    • schrodinger.application.licensing.flexlm.Vendor: Vendor objects represent VENDOR lines in the license file.
  • schrodinger.application.licensing.licadmin.LicenseResource: A LicenseResource object represents a single license file or license server (port@host).
  • schrodinger.application.matsci.buildcomplex.Ligand: Stores information about a ligand structure
  • schrodinger.application.bioluminate.pml_menus.LigandActionMixin: Class that contains a method to restrict the asl to Ligands only
  • schrodinger.application.desmond.replica_sid_generator.LigandReport
  • schrodinger.infra.mmkv.MMKVArgList: A class to provide list-like access to MMKV/MMIM array properties.
  • schrodinger.utils.colorscheme.MM_CScheme
  • schrodinger.utils.colorscheme.MM_CSchemeRule
  • schrodinger.utils.colorscheme.MM_Color
  • schrodinger.utils.colorscheme.MM_ColorRamp
  • schrodinger.utils.colorscheme.MM_ColorRampHolder
  • schrodinger.utils.colorscheme.MM_Colormap
    • schrodinger.utils.colorscheme.MM_ColormapGL
  • schrodinger.utils.colorscheme.MMrange
  • schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackMixin: A mixin that allows the above decorators to be used for maestro callbacks.
  • schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator
  • schrodinger.application.desmond.starter.generator.fep_plus.MapperRestartGenerator
  • schrodinger.maestro.markers.Marker: Class to manipulate a set of markers in the Workspace by ASLs.
  • schrodinger.ui.qt.appframework2.markers.MarkerMixin: A mixin for adding markers and controlling their visibility.
  • schrodinger.application.jaguar.gui.base_panel.MarkerMixin: A mixin for panels that want markers displayed only when certain tabs are active.
  • 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.application.desmond.fep_scholar_util.MetaAtom: This is the meta atom class that mostly provides convinience functions.
  • schrodinger.infra.mmobject.MmObject: An abstraction of the bookkeeping needed to create a garbage collected MM object.
  • schrodinger.trajectory.prody.modeset.ModeSet: A class for providing access to subset of mode data.
  • 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.matsci.nano.xtal.CrystalSystems.Monoclinic: Manage the monoclinic system.
  • schrodinger.application.mopac.results2012.Mopac2012TextParser: Parser for the MOPAC2012 .out and .aux files.
  • schrodinger.application.mopac.mopac_api.MopacAPI: This class is an API for the MOPAC backend.
  • schrodinger.application.mopac.mopac_launchers.MopacLauncher: This abstract base class (ABC) is designed to guide developers writing code to support future MOPAC releases.
  • schrodinger.application.mopac.mopac_results.MopacResults: This abstract base class (ABC) is designed to guide developers writing code to support future MOPAC releases.
  • schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin: A mixin for panels that contain a MultiStructureTab.
  • schrodinger.application.matsci.nano.tube.MultiWalledNanoTube: Build a multi-walled nanotube by assembling specific NanoTubes.
  • schrodinger.trajectory.prody.nma.NMA: A class for handling Normal Mode Analysis (NMA) data.
  • schrodinger.application.matsci.nano.tube.NanoSheet: Create a sheet.HoneycombLattice that is large enough so that the nanotube sheet can be cut out from it.
  • schrodinger.application.matsci.nano.sheet.NanoSheets: Main class for making nanosheets.
  • schrodinger.application.matsci.nano.tube.NanoTube: Create a nanotube by rolling up a nanotube sheet.
  • schrodinger.application.matsci.nano.tube.NanoTubeSheet: Preprocess a nanosheet into a nanotube sheet which will be rolled up into a nanotube.
  • schrodinger.application.matsci.nano.tube.NanoTubes: Main class for making nanotubes.
  • schrodinger.application.matsci.nano.particle.Nanoparticle: Manage the building of a nanoparticle.
  • schrodinger.application.matsci.nano.sheet.NeighborType: Manage the properties of a neighbor type.
  • schrodinger.application.desmond.maestro.NewEntry: A class for representing a structure that can be included/excluded in the Workspace.
  • schrodinger.application.desmond.maestro.NewEntryGroup: A class for representing a group of Structures that can be included in or excluded from the Workspace as requested.
  • schrodinger.application.jaguar.gui.base_panel.NoInputTabJobMixin: A mixin that will add the standard Jaguar job running and writing behavior.
  • schrodinger.application.desmond.reorder_atom.Node
  • schrodinger.application.desmond.enhsamp.Node
  • schrodinger.application.desmond.feputils.OPLSSettingManager: Simple context manager to modify and restore user's OPLS_DIR setting, if appropriate.
  • schrodinger.application.matsci.nano.xtal.CrystalSystems.Orthorhombic: Manage the orthorhombic system.
  • schrodinger.application.matsci.nano.xtal.PBCBond: Class to manage a PBC bond, i.e.
  • schrodinger.application.matsci.nano.xtal.PBCBonds: Class to manage a collection of PBC bonds.
  • schrodinger.application.matsci.nano.slab.ParserWrapper: Manages the argparse module to parse user command line arguments.
  • schrodinger.application.matsci.nano.surfaces_interfaces_mod.ParserWrapper: Manages the argparse module to parse user command line arguments.
  • schrodinger.application.matsci.nano.interface_mod.ParserWrapper: Manages the argparse module to parse user command line arguments.
  • schrodinger.application.matsci.nano.xtal.ParserWrapper: Manages the argparse module to parse user command line arguments.
  • schrodinger.application.matsci.nano.particle.ParserWrapper: Manages the argparse module to parse user command line arguments.
  • schrodinger.application.matsci.rxn_path.ParserWrapper: Manages the argparse module to parse user command line arguments.
  • schrodinger.application.phase.phase_markers.PhaseFeatureMixin: A mixin for adding pharmacophore feature markers and controlling their visibility.
  • schrodinger.infra.phase.PhpFeatureData: Proxy of C++ PhpFeatureData class
  • schrodinger.infra.phase.PhpFeatureDefinition: Proxy of C++ PhpFeatureDefinition class
  • schrodinger.infra.phase.PhpProject: Proxy of C++ PhpProject class
  • schrodinger.infra.phase.PhpSite: Proxy of C++ PhpSite class
  • schrodinger.application.desmond.picklejar.Picklable
  • schrodinger.application.desmond.picklejar.PickleJar
  • schrodinger.application.desmond.picklejar.PickleState
  • schrodinger.application.report2d.PicturePrinter: Class for drawing structure pictures to a QPrinter for generating PDFs.
  • schrodinger.analysis.enrichment.Plotter: A class to plot multiple series of Calculator data.
  • schrodinger.application.matsci.rxn_path.Point: Collect properties of reaction path points.
  • 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.application.matsci.rxn_channel.rxn_channel.Products: Manage the properties of the products that result from applying a reaction channel definition to the reactants.
  • schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry: A class for accessing data about a project table row and the associated structure
  • schrodinger.project.ProjectRow: ProjectRow allows access to the structure and properties of an entry in the project.
  • schrodinger.application.jaguar.gui.base_panel.PropertiesMixin: A mixin that will send updates the Properties tab whenever the relevant settings in the "Theory" or "Molecule" tab change.
  • schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property: Manage a property to be used in a genetic optimization.
  • schrodinger.application.bioluminate.protein.PropertyCalculator: Class for calculating properties of proteins and protein residues.
  • schrodinger.protein.reliability.ProteinCheckParameters
  • schrodinger.application.desmond.replica_sid_generator.ProteinReport
  • schrodinger.test.structurecheck.ProteinReportCheck: This is a wrapper for ProteinReport which is used for unittesting and scientific testing.
  • schrodinger.application.desmond.cms.Pseudo
  • schrodinger.utils.pymol.PymolInstance: Represents a remote PyMOL instance (controlled via a one-way pipe)
  • schrodinger.application.desmond.cmj.Queue
  • schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule: Manage a reactant molecule in the reactants structure object.
  • schrodinger.application.matsci.rxn_channel.rxn_channel.Reactants: Manage the properties of the reactants.
  • schrodinger.application.matsci.rxn_path.ReactionCoords: Manage reaction coordinates.
  • schrodinger.application.matsci.rxn_path.ReactionPath: Generate reaction path.
  • schrodinger.application.jaguar.gui.base_panel.ReadEditMixin: A mixin for panels that should include Read...
  • 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.matsci.nano.tube.Rectangle: Manage the properties of a rectangle.
  • schrodinger.application.bioluminate.pml_menus.RegionInfo
  • schrodinger.application.desmond.gui.RelaxFrame: Frame that includes the "Relax model..." check box and the relaxation protocol entry field.
  • schrodinger.application.desmond.stage.Reporter
  • schrodinger.ui.residueselector.ResidueGroups: Class representing the residue "groups" that appear as mixed-state checkboxes in the residue selector pop-up.
  • schrodinger.application.desmond.cms.Restrain
  • schrodinger.test.stu.client.ResultReporter: Reporter that will upload results and files for a specific test run.
  • schrodinger.application.matsci.jaguarworkflows.Results: A low memory results object - because the driver ends up holding on to results for a long time and can be simultaneously holding results for a large number of calculations, we want to keep the memory footprint of each result low.
  • schrodinger.protein.reliability.Results: The Results object stores the results from a protein health check.
  • 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.test.stu.run.Runner: Runner controls all job running parameters within the backend test utility code.
  • schrodinger.application.matsci.amorphous.Scaffold: A Scaffold is a structure that occupies space in a cluster of molecules but is not considered part of the system itself.
  • schrodinger.application.jaguar.scan.Scan: A class for storing information about geometry scan variables.
  • 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.Hydrogen
    • 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.application.licensing.licadmin.ServerInfo: A ServerInfo object represents the information reported in the lmgrd log when a license server is started.
  • schrodinger.application.jaguar.keywordDB.Setting: A class to hold keyword setting info.
  • schrodinger.ui.qt.appframework2.settings.SettingsMixin: Mixin allows an object to save/restore its own state to/from a dictionary.
  • schrodinger.application.desmond.gui.SimOptionsFrame: Responsible for drawing the simulation options widgets, including Simulation time and Recording intervals.
  • schrodinger.application.desmond.cms.Site
  • schrodinger.application.matsci.genetic_optimization.genetic_optimization.Skip: Manage a skip.
  • schrodinger.application.bioluminate.sliderchart.SlidableLine: A line on a matplotlib plot that can be grabbed and moved by the user
  • schrodinger.application.matsci.nano.xtal.SpaceGroup: Collect the properties of a space group.
  • schrodinger.application.matsci.nano.xtal.SpaceGroups: Manage space group objects.
  • schrodinger.structutils.ringspear.Spear: Contains the atom indexes involved in a ring spear and formats the data in a user-readable string
  • schrodinger.structutils.ringspear.SpearRing: Computes and holds information about a ring, and finds bonds that spear that ring.
  • schrodinger.application.ligprep.ionizer.Spec: This class represents a specification line in the ionizer data file.
  • schrodinger.application.matsci.shapes.Sphere: Class to manage a sphere.
  • schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController: Controller to facilitate interaction between widget that defines spin treatment options and excited state widget.
  • schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns: Constants for the split table columns (i.e.
  • schrodinger.application.jaguar.gui.base_panel.StandardStatusMixin: A mixin that will add the standard Jaguar status bar text to a Jaguar panel.
  • schrodinger.ui.appframework.StartDialogParams: A collection of parameter values from the StartDialog class.
  • schrodinger.application.desmond.starter.starter.Starter
  • schrodinger.application.desmond.multisimstartup.Startup
  • schrodinger.application.licensing.licadmin.Status: A Status object represents the "health" of a license resource.
  • schrodinger.application.matsci.jaguarworkflows.Step: Manages the start, monitoring and finish of a single step in a workflow
  • schrodinger.application.matsci.jobutils.StringCleaner: Manages the cleaning of strings.
  • 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.desmond.fep_struc.Struc
    • schrodinger.application.desmond.fep_struc.SchrodStruc: A `Struc' subclass based on Schrodinger's infrastructure
  • 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.application.desmond.stage.FepAnalysis.Structure
  • schrodinger.application.mopac.structure_launchers.StructureLauncher: A class for running MOPAC calculations on a Structure object.
  • schrodinger.application.jaguar.gui.base_panel.SubTabMixin: A mixin for panels that contain an InputTab with sub-tabs.
  • schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow: An object representing a single row of the table.
  • schrodinger.surface.Surface: A Pythonic wrapping for mmsurf surfaces that are not associated with a project entry.
  • schrodinger.application.matsci.nano.slab.Surface: Manage the building of a surface model.
  • schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces: Manage the enumeration of surfaces.
  • schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces: Manage the enumeration of surfaces and interfaces.
  • schrodinger.infra.mmsurf.SwigDoubleVector
  • schrodinger.utils.colorscheme.SwigDoubleVector
  • schrodinger.infra.phase.SwigDoubleVector: Proxy of C++ std::vector<(double)> class
  • schrodinger.infra.mmgpgpu.SwigDoubleVector
  • schrodinger.infra.mmsurf.SwigDoubleVector3
  • schrodinger.infra.mmgpgpu.SwigDoubleVector3
  • schrodinger.utils.colorscheme.SwigDoubleVector3
  • schrodinger.infra.phase.SwigDoubleVector3: Proxy of C++ std::vector<(std::vector<(std::vector<(double)>)>)> class
  • schrodinger.utils.colorscheme.SwigIntIntPair
  • schrodinger.infra.mmsurf.SwigIntIntPair
  • schrodinger.infra.mmgpgpu.SwigIntIntPair
  • schrodinger.infra.phase.SwigIntIntPair: Proxy of C++ std::pair<(int,int)> class
  • schrodinger.infra.phase.SwigIntVector: Proxy of C++ std::vector<(int)> class
  • schrodinger.infra.mmgpgpu.SwigIntVector
  • schrodinger.infra.mmsurf.SwigIntVector
  • schrodinger.utils.colorscheme.SwigIntVector
  • schrodinger.utils.colorscheme.SwigPyIterator
  • schrodinger.trajectory.rdf_backend.SwigPyIterator
  • schrodinger.infra.mmsurf.SwigPyIterator
  • schrodinger.infra.phase.SwigPyIterator: Proxy of C++ swig::SwigPyIterator class
  • schrodinger.infra.mmgpgpu.SwigPyIterator
  • schrodinger.utils.mmutil.SwigPyIterator
  • unreachable.SwigPyObject: Swig object carries a C/C++ instance pointer
    • schrodinger.infra.structure.AtomPairWithValue: schrodinger::structure_interaction::AtomPairWithValue
    • schrodinger.infra.structure.AtomQueryParams: schrodinger::structure_interaction::AtomQueryParams
    • schrodinger.infra.structure.CellMatchAtom: schrodinger::CellMatchAtom
    • schrodinger.infra.structure.ContactParams: schrodinger::structure_interaction::ContactParams
      • schrodinger.infra.structure.SaltBridgeParams: schrodinger::structure_interaction::SaltBridgeParams
    • schrodinger.infra.structure.DistanceCell: schrodinger::DistanceCell
    • schrodinger.infra.structure.DoubleDoubleList: std::vector< std::vector< double > >
    • schrodinger.infra.structure.DoubleList: std::vector< double >
    • schrodinger.infra.structure.IOException: schrodinger::IOException
      • schrodinger.infra.structure.StructureReaderException: schrodinger::StructureReaderException
    • schrodinger.infra.structure.InteractionAtomPair: schrodinger::structure_interaction::InteractionAtomPair
      • schrodinger.infra.structure.SaltBridge: schrodinger::structure_interaction::SaltBridge
    • schrodinger.infra.structure.Mmpdbx: schrodinger::Mmpdbx
    • schrodinger.infra.structure.PBC: schrodinger::PBC
    • schrodinger.infra.structure.PdbMmpdbxAtom: ::PdbMmpdbxAtom
      • schrodinger.infra.structure.MmpdbxAtom: schrodinger::MmpdbxAtom
    • schrodinger.infra.structure.PiCationInteraction: schrodinger::structure_interaction::PiCationInteraction
    • schrodinger.infra.structure.PiCationParams: schrodinger::structure_interaction::PiCationParams
    • schrodinger.infra.structure.PiPiInteraction: schrodinger::structure_interaction::PiPiInteraction
    • schrodinger.infra.structure.PiPiParams: schrodinger::structure_interaction::PiPiParams
    • schrodinger.infra.structure.StringList: std::vector< std::string >
    • schrodinger.infra.structure.Structure: schrodinger::Structure
    • schrodinger.infra.structure.StructureAtom: schrodinger::StructureAtom
    • schrodinger.infra.structure.StructureIterator: schrodinger::StructureIterator
    • schrodinger.infra.structure.StructureReader: schrodinger::StructureReader
      • schrodinger.infra.structure.StructureFileReader: schrodinger::StructureFileReader
        • schrodinger.infra.structure.MaestroReader: schrodinger::MaestroReader
        • schrodinger.infra.structure.MmpdbxReader: schrodinger::MmpdbxReader
        • schrodinger.infra.structure.Mol2Reader: schrodinger::Mol2Reader
        • schrodinger.infra.structure.PdbReader: schrodinger::PdbReader
        • schrodinger.infra.structure.SdReader: schrodinger::SdReader
    • schrodinger.infra.structure.StructureRing: schrodinger::StructureRing
    • schrodinger.infra.structure.SwigAtomList: std::vector< schrodinger::StructureAtom >
    • schrodinger.infra.structure.SwigAtomPairList: std::vector< schrodinger::structure_interaction::InteractionAtomPair >
    • schrodinger.infra.structure.SwigAtomPairWithValueList: std::vector< schrodinger::structure_interaction::AtomPairWithValue >
    • schrodinger.infra.structure.SwigAtomQueryParamsList: std::vector< boost::shared_ptr< schrodinger::structure_interaction::AtomQueryParams > >
    • schrodinger.infra.structure.SwigDcNonPbcAtomIdxList: std::vector< int >
    • schrodinger.infra.structure.SwigDcPbcAtomList: std::vector< schrodinger::CellMatchAtom >
    • schrodinger.infra.structure.SwigPiCationList: std::vector< schrodinger::structure_interaction::PiCationInteraction >
    • schrodinger.infra.structure.SwigPiPiInteractionList: std::vector< schrodinger::structure_interaction::PiPiInteraction >
    • schrodinger.infra.structure.SwigPyIterator: swig::SwigPyIterator
    • schrodinger.infra.structure.SwigRingList: std::vector< boost::shared_ptr< schrodinger::StructureRing > >
    • schrodinger.infra.structure.SwigSaltBridgeList: std::vector< schrodinger::structure_interaction::SaltBridge >
  • schrodinger.infra.phase.SwigStringVector: Proxy of C++ std::vector<(std::string)> class
  • schrodinger.utils.colorscheme.SwigStringVector
  • schrodinger.infra.mmgpgpu.SwigStringVector
  • schrodinger.infra.mmsurf.SwigStringVector
  • schrodinger.infra.phase.SwigUInt64Vector: Proxy of C++ std::vector<(uint64,std::allocator<(uint64)>)> class
  • schrodinger.infra.mmgpgpu.SwigUInt64Vector
  • schrodinger.utils.colorscheme.SwigUInt64Vector
  • schrodinger.infra.mmsurf.SwigUInt64Vector
  • schrodinger.infra.mmsurf.SwigUnsignedIntVector
  • schrodinger.infra.mmgpgpu.SwigUnsignedIntVector
  • schrodinger.infra.phase.SwigUnsignedIntVector: Proxy of C++ std::vector<(unsigned int)> class
  • schrodinger.utils.colorscheme.SwigUnsignedIntVector
  • schrodinger.infra.mmsurf.SwigUnsignedIntVector2
  • schrodinger.utils.colorscheme.SwigUnsignedIntVector2
  • schrodinger.infra.phase.SwigUnsignedIntVector2: Proxy of C++ std::vector<(std::vector<(unsigned int)>)> class
  • schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2
  • schrodinger.infra.mmgpgpu.SwigVectorIntIntPair
  • schrodinger.utils.colorscheme.SwigVectorIntIntPair
  • schrodinger.infra.phase.SwigVectorIntIntPair: Proxy of C++ std::vector<(std::pair<(int,int)>)> class
  • schrodinger.infra.mmsurf.SwigVectorIntIntPair
  • schrodinger.application.matsci.nano.sheet.SymmetryEquiv: Manage symmetry equivalent positions in the unit cell.
  • 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.matsci.builderwidgets.TMLigandRowMixin: A mixin class that takes care of minimizing bidentate transition metal complex ligand structures so that they remain planar through the R1-...-R2 bond path.
  • schrodinger.application.jaguar.gui.base_panel.TaskStatusMixin: A mixin that will add the task name to the status bar text.
  • 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.test.performance.reporter.Test: A performance test.
  • schrodinger.test.stu.run.TestJob: Interface for the TestJCJob and TestSPJob classes
  • schrodinger.test.stu.testscripts.TestScript
  • schrodinger.application.desmond.util.TestSuite: A small and tight class designed for unit tests.
  • schrodinger.test.stu.base_executable.TestUtility
  • schrodinger.application.matsci.nano.xtal.CrystalSystems.Tetragonal: Manage the tetragonal system.
  • 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.matsci.nano.xtal.CrystalSystems.Triclinic: Manage the triclinic system.
  • schrodinger.application.matsci.nano.xtal.CrystalSystems.Trigonal: Manage the trigonal system.
  • schrodinger.application.desmond.systype.TyperBase
  • schrodinger.application.desmond.starter.ui.fep_plus.UI
  • schrodinger.application.desmond.starter.ui.multisim.UI
  • schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog
  • schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui.Ui_Dialog
  • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_constraints_ui.Ui_Dialog
  • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_collection_viewer_ui.Ui_Dialog
  • schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog
  • schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog
  • schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui.Ui_Form
  • schrodinger.ui.ligfilter_ui.Ui_Form
  • schrodinger.application.prime.gui.ui.analyze_energy_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.reaction_tab_ui.Ui_Form
  • schrodinger.application.bioluminate.propfilter_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.irc_top_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.optimization_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.scf_tab_ui.Ui_Form
  • schrodinger.application.desmond.rest_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui.Ui_Form
  • schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.scan_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.properties_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.molecule_top_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.input_top_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.irc_bottom_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.multi_structures_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui.Ui_Form
  • schrodinger.application.desmond.input_group_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.transition_state_top_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.input_std_bottom_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.solvent_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.theory_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui.Ui_Form
  • schrodinger.application.prime.gui.ui.environment_options_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.output_tab_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui.Ui_Form
  • schrodinger.application.jaguar.gui.ui.edit_dialog_ui.Ui_MainWindow
  • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_cfc_ui.Ui_Widget
  • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_ui.Ui_Widget
  • schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui.Ui_Widget
  • schrodinger.application.jaguar.gui.ui.excited_state_widget_ui.Ui_Widget
  • schrodinger.application.jaguar.gui.base_panel.UseConsistentOrbitalsMixin: A mixin for panels where the SCF tab contains a "Use consistent orbitals" checkbox.
  • schrodinger.application.desmond.cms.Vdw: A class for handling VDW parameters.
  • schrodinger.trajectory.prody.mode.VectorBase: A base class for :class:`Mode` and :class:`Vector`.
  • schrodinger.application.matsci.shapes.Vertex: Class to manage vertices.
  • schrodinger.utils.pymol.VisRecord: Represents a surface entry in a "vis_list" file
  • schrodinger.analysis.visanalysis.volumedata.VolumeData: The VolumeData class is responsible for handling the underlying storage as well as marrying together the concepts of array-coordinates and world-coordinates.
  • schrodinger.protein.getpdb_utility.WholePDB: Class to take care of the file work for entire PDB files.
  • schrodinger.ui.widgettable.WidgetTable: The table class with scroll bars
  • schrodinger.application.matsci.jaguarworkflows.WorkFlow: A class to hold the data for and shepherd a single structure through all the jobs required to gather its data.
  • schrodinger.application.desmond.maestro.Workspace: A class for representing the Workspace.
  • schrodinger.utils.pymol.WorkspaceIdMapper: Maps workspace atom indices to (row.index, ID)
  • schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler: Class with methods for manipulating workspace atom labels.
  • schrodinger.application.matsci.zmutils.ZAtom: A single atom in a Z-matrix
  • schrodinger.application.matsci.zmutils.ZMatrix: Contains the z-matrix for a structure
  • argparse._ActionsContainer
  • schrodinger.application.desmond.gui._AtomGroup: Represents the data of the atom group table? Of the Misc tab of the Advanced Options dialog
  • argparse._AttributeHolder: Abstract base class that provides __repr__.
  • schrodinger.job.jobcontrol._Backend: An interface to mmjobbe.
  • schrodinger.application.desmond.gui._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
  • schrodinger.test.stu.client._BaseClient: Base client class providing some reasonable defaults.
  • schrodinger.application.desmond.gui._BaseGroup: Inherited by MdGroup and MinimizeGroup, so therefore by all Simulation frames
  • schrodinger.maestro.markers._BaseMarker: Base class for the marker classes.
  • schrodinger.application.desmond.mdkey._Bool
  • unreachable._CData: XXX to be provided
    • _ctypes.Structure: Structure base class
      • schrodinger.test.darwinconsole.Utmpx: This struct utmpx definition is only correct on Darwin.
  • 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._DummyMaestroModule: Used to replace schrodinger.maestro.maestro when running outside of Maestro.
  • schrodinger.application.licensing.licerror._ErrorLevel: An _ErrorLevel is an ordered type that represents the severity of a license error.
  • schrodinger.job.host_check._ErrorLevel: An ErrorLevel is an ordered type that represents the severity of a host-check error.
  • schrodinger.application.desmond.mdkey._Evalor
  • schrodinger.utils.sea._Evalor: This is the evaluator class for checking validity of parameters.
  • 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.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.test.stu.sysinfo._FakeLocal: Lazily evaluated local host.
  • schrodinger.test.stu.sysinfo._FakeRemote: Lazily evaluated remote host.
  • 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.test.stu.outcomes.job_status._LicenseInfo: Extract an in-memory representation of the license checkouts from a named license checkout file.
  • schrodinger.analysis.visanalysis.volumedataio._MMInitialiser: The _MMInitialiser class exists solely to initialise and terminate the mmlibs correctly.
  • schrodinger.analysis.visanalysis.volumedataio._MMVol: The _MMVol class acts as a wrapper around low-level MMVol objects.
  • schrodinger.application.desmond.antlr3.main._Main
  • schrodinger.application.desmond.gui._MdcBase: The Advanced options dialogs and their tab widgets subclass this class.
  • schrodinger.structutils.createfragments._Options: A class to hold a list of options.
  • schrodinger.ui.picking._PickToggle: Base class for picking toggles.
    • schrodinger.ui.picking.Pick3DObjectToggle: Class meant to replicate a Maestro pick toggle.
    • 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.ui.picking.PickMixedToggle: Class allowing to pick atom or bond depending on internal state.
    • schrodinger.ui.picking.PickTorsionToggle: Class for creating a picker that allows the user to define a torsion by sequentually picking 4 atoms.
  • schrodinger.structure._ReaderWriterContextManager: A mixin to enable context manager usage in reader and writer classes.
  • 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.ska._SkaData: Data structure for named backend return values...
  • schrodinger.structutils.createfragments._StructureFragmenter: Class to create fragments from a given set of _Options and a given schrodinger.structure.Structure.
  • schrodinger.test.stu.sysinfo._SysInfo: Determines and saves the system information.
  • schrodinger.analysis.visanalysis.vdaxis._VDAxis: The _VDAxis class represents a single coordinate-axis.
  • schrodinger.analysis.visanalysis.vdcoordinateframe._VDCoordinateFrame: The _VDCoordinateFrame class is primarily a utility class.
  • schrodinger.ui.qt.pop_up_widgets._WidgetWithPopUpMixin: Container for methods shared between ComboBoxWithPopUp and LineEditWithPopUp classes.
  • schrodinger.application.desmond.cmj._create_param_when_needed
  • schrodinger.application.desmond.config._create_when_needed
  • schrodinger.application.desmond.envir._create_when_needed
  • schrodinger.application.desmond.cmj._get_jc_backend_when_needed
  • basestring: Type basestring cannot be instantiated; it is the base for str and unicode.
    • str: str(object) -> string
      • 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
  • schrodinger.utils.fileutils.chdir: A context manager that carries out commands inside of the specified directory and restores the current directory when done.
  • 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.
    • schrodinger.application.desmond.fepdiff.FEPIOProperty
    • schrodinger.application.desmond.fepdiff.FFIOProperty
    • schrodinger.application.desmond.fepdiff.IndexDict
    • 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.prime.input.Prime: Class for reading and writing simplified Prime input files.
    • schrodinger.test.stu.outcomes.compareDesmondSystems.System: A very basic class to hold cms data.
    • 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
  • schrodinger.application.combiglide.combenumdock.glidePrecisionDialog
  • int: int(x[, base]) -> integer
    • PyQt4.QtGui.QAction.ActionEvent
    • PyQt4.QtGui.QGraphicsItem.CacheMode
    • PyQt4.QtGui.QGraphicsView.CacheModeFlag
    • PyQt4.QtGui.QAbstractItemView.CursorAction
    • PyQt4.QtGui.QDialog.DialogCode
    • PyQt4.QtGui.QMainWindow.DockOption
    • PyQt4.QtGui.QAbstractItemView.DragDropMode
    • PyQt4.QtGui.QGraphicsView.DragMode
    • PyQt4.QtGui.QAbstractItemView.DropIndicatorPosition
    • PyQt4.QtGui.QAbstractItemView.EditTrigger
    • PyQt4.QtGui.QGraphicsItem.GraphicsItemChange
    • PyQt4.QtGui.QGraphicsItem.GraphicsItemFlag
    • enum.IntEnum: Enum where members are also (and must be) ints
    • PyQt4.QtGui.QGraphicsScene.ItemIndexMethod
    • schrodinger.ui.maestroui.MMENUM_DGO_CHANGED_TYPE
    • PyQt4.QtGui.QAction.MenuRole
    • PyQt4.QtGui.QGraphicsView.OptimizationFlag
    • PyQt4.QtGui.QPaintDevice.PaintDeviceMetric
    • PyQt4.QtGui.QGraphicsItem.PanelModality
    • PyQt4.QtGui.QAction.Priority
    • PyQt4.QtGui.QWidget.RenderFlag
    • PyQt4.QtGui.QGraphicsScene.SceneLayer
    • 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.QAction.SoftKeyRole
    • PyQt4.QtGui.QAbstractItemView.State
    • PyQt4.QtGui.QFrame.StyleMask
    • PyQt4.QtGui.QGraphicsView.ViewportAnchor
    • PyQt4.QtGui.QGraphicsView.ViewportUpdateMode
    • schrodinger.ui.sketcher.sketcherMouseAction
  • schrodinger.infra.phase.istream: Proxy of C++ std::istream class
    • schrodinger.infra.phase.ifstream: Proxy of C++ std::ifstream class
  • schrodinger.infra.mmsurf.istream
  • schrodinger.utils.colorscheme.istream
    • schrodinger.utils.colorscheme.ifstream
  • schrodinger.infra.mmgpgpu.istream
  • list: list() -> new empty list list(iterable) -> new list initialized from iterable's items
    • schrodinger.utils.sea.List: This class represents the "list" parameters in a config file.
    • schrodinger.infra.util.OneIndexedList: A list that starts at one instead of zero
  • schrodinger.infra.mmgpgpu.ostream
  • schrodinger.utils.colorscheme.ostream
    • schrodinger.utils.colorscheme.ofstream
      • schrodinger.utils.colorscheme.TemporaryOFStream: A subclass of ofstream that uses the tempfile module to get a temporary filename and automatically deletes itself at garbage collection.
  • schrodinger.infra.phase.ostream: Proxy of C++ std::ostream class
    • schrodinger.infra.phase.ofstream: Proxy of C++ std::ofstream class
      • schrodinger.infra.phase.TemporaryOFStream: A subclass of ofstream that uses the tempfile module to get a temporary filename and automatically deletes itself at garbage collection.
  • schrodinger.infra.mmsurf.ostream
  • property: property(fget=None, fset=None, fdel=None, doc=None) -> property attribute
  • schrodinger.application.desmond.replica_dE.replica_container
  • schrodinger.application.desmond.replica_dE.replica_energy
  • schrodinger.application.desmond.replica_dE.replicas_monitor
  • 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.QAbstractItemView.EditTriggers: QAbstractItemView.EditTriggers(QAbstractItemView.EditTriggers) QAbstractItemView.EditTriggers(int) QAbstractItemView.EditTriggers()
    • PyQt4.QtGui.QGraphicsItem.GraphicsItemFlags: QGraphicsItem.GraphicsItemFlags(QGraphicsItem.GraphicsItemFlags) QGraphicsItem.GraphicsItemFlags(int) QGraphicsItem.GraphicsItemFlags()
    • PyQt4.QtGui.QGraphicsView.OptimizationFlags: QGraphicsView.OptimizationFlags(QGraphicsView.OptimizationFlags) QGraphicsView.OptimizationFlags(int) QGraphicsView.OptimizationFlags()
    • PyQt4.QtGui.QPaintDevice: QPaintDevice()
      • PyQt4.QtGui.QWidget: QWidget(QWidget parent=None, Qt.WindowFlags flags=0)
        • schrodinger.application.bioluminate.antibody.search_results_table.FullTable: A widget to contain the full search results table
        • PyQt4.QtGui.QDialog: QDialog(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog: A dialog for showing exceptions to users
        • PyQt4.QtGui.QFrame: QFrame(QWidget parent=None, Qt.WindowFlags flags=0)
          • PyQt4.QtGui.QAbstractScrollArea: QAbstractScrollArea(QWidget parent=None)
            • PyQt4.QtGui.QAbstractItemView: QAbstractItemView(QWidget parent=None)
              • PyQt4.QtGui.QTableView: QTableView(QWidget parent=None)
                • schrodinger.application.bioluminate.antibody.search_results_table.TableView: A table view for both full and split search results.
            • PyQt4.QtGui.QGraphicsView: QGraphicsView(QWidget parent=None) QGraphicsView(QGraphicsScene, QWidget parent=None)
              • schrodinger.ui.dendro.DendrogramView
              • schrodinger.ui.sketcher.sketcherView
        • PyQt4.QtGui.QMainWindow: QMainWindow(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.ui.sketcher.sketcher
        • PyQt4.QtGui.QToolBar: QToolBar(QString, QWidget parent=None) QToolBar(QWidget parent=None)
          • schrodinger.ui.sketcher.sketcherGUIMultiColumnToolBar
        • schrodinger.application.bioluminate.antibody.search_results_table.SplitTable: A widget to contain both split search results tables (i.e.
    • PyQt4.QtGui.QWidget.RenderFlags: QWidget.RenderFlags(QWidget.RenderFlags) QWidget.RenderFlags(int) QWidget.RenderFlags()
    • PyQt4.QtGui.QGraphicsScene.SceneLayers: QGraphicsScene.SceneLayers(QGraphicsScene.SceneLayers) QGraphicsScene.SceneLayers(int) QGraphicsScene.SceneLayers()
    • sip.wrapper
      • schrodinger.ui.dendro.DendrogramGraphicTreeCoordinatesPreferences
      • schrodinger.ui.dendro.DendrogramNode
      • schrodinger.ui.dendro.DendrogramNodeBFIterator
      • schrodinger.ui.dendro.DendrogramTreeBuilder
      • schrodinger.infra.projectmodel.schrodinger.MM_Project
      • schrodinger.ui.maestroui.MM_UIAbstractPropertyManager
      • PyQt4.QtGui.QGraphicsItem: QGraphicsItem(QGraphicsItem parent=None, QGraphicsScene scene=None)
        • schrodinger.ui.dendro.DendrogramGraphicNodeLabel
        • PyQt4.QtGui.QGraphicsItemGroup: QGraphicsItemGroup(QGraphicsItem parent=None, QGraphicsScene scene=None)
          • schrodinger.ui.dendro.DendrogramGraphicTree
        • PyQt4.QtGui.QGraphicsObject: QGraphicsObject(QGraphicsItem parent=None)
          • schrodinger.ui.dendro.DendrogramGraphicNode
        • schrodinger.ui.sketcher.sketcherGraphicalObject
          • schrodinger.ui.sketcher.sketcherAtom
            • schrodinger.ui.sketcher.sketcherResidue
          • schrodinger.ui.sketcher.sketcherBond
            • schrodinger.ui.sketcher.sketcherResidueInteraction
      • PyQt4.QtCore.QObject: QObject(QObject parent=None)
        • schrodinger.application.combiglide.connection_storage.ConnectionStorage: This class is used to store the data of the current connection table.
        • schrodinger.ui.dendro.DendrogramGraphicTree
        • schrodinger.ui.maestroui.MM_StructMonitor
        • schrodinger.ui.maestroui.MM_UIBasic
          • schrodinger.ui.maestroui.MM_UIComponent
            • schrodinger.ui.maestroui.MM_UIForm
              • schrodinger.ui.maestroui.MM_UIVBoxLayout
                • schrodinger.ui.maestroui.MM_UIAbstractPropertySelector
                  • schrodinger.ui.maestroui.MM_UICompactPropertySelector
        • PyQt4.QtCore.QAbstractItemModel: QAbstractItemModel(QObject parent=None)
          • PyQt4.QtGui.QAbstractProxyModel: QAbstractProxyModel(QObject parent=None)
            • PyQt4.QtGui.QSortFilterProxyModel: QSortFilterProxyModel(QObject parent=None)
              • schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel: A proxy model for the full search results.
                • schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel: A proxy for the split search results (i.e.
          • PyQt4.QtCore.QAbstractTableModel: QAbstractTableModel(QObject parent=None)
            • schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel: A model to store search results
          • PyQt4.QtGui.QStandardItemModel: QStandardItemModel(QObject parent=None) QStandardItemModel(int, int, QObject parent=None)
            • schrodinger.infra.projectmodel.RowModel
        • PyQt4.QtGui.QAction: QAction(QObject) QAction(QString, QObject) QAction(QIcon, QString, QObject)
          • schrodinger.application.bioluminate.actions.factory.SAction: A QAction that enforces standards that are expected by some BioLuminate methods.
        • PyQt4.QtGui.QGraphicsObject: QGraphicsObject(QGraphicsItem parent=None)
          • schrodinger.ui.dendro.DendrogramGraphicNode
        • PyQt4.QtGui.QGraphicsScene: QGraphicsScene(QObject parent=None) QGraphicsScene(QRectF, QObject parent=None) QGraphicsScene(float, float, float, float, QObject parent=None)
          • schrodinger.ui.dendro.DendrogramScene
          • schrodinger.ui.sketcher.sketcherScene
        • PyQt4.QtGui.QWidget: QWidget(QWidget parent=None, Qt.WindowFlags flags=0)
          • schrodinger.application.bioluminate.antibody.search_results_table.FullTable: A widget to contain the full search results table
          • PyQt4.QtGui.QDialog: QDialog(QWidget parent=None, Qt.WindowFlags flags=0)
            • schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog: A dialog for showing exceptions to users
          • PyQt4.QtGui.QFrame: QFrame(QWidget parent=None, Qt.WindowFlags flags=0)
            • PyQt4.QtGui.QAbstractScrollArea: QAbstractScrollArea(QWidget parent=None)
              • PyQt4.QtGui.QAbstractItemView: QAbstractItemView(QWidget parent=None)
                • PyQt4.QtGui.QTableView: QTableView(QWidget parent=None)
                  • schrodinger.application.bioluminate.antibody.search_results_table.TableView: A table view for both full and split search results.
              • PyQt4.QtGui.QGraphicsView: QGraphicsView(QWidget parent=None) QGraphicsView(QGraphicsScene, QWidget parent=None)
                • schrodinger.ui.dendro.DendrogramView
                • schrodinger.ui.sketcher.sketcherView
          • PyQt4.QtGui.QMainWindow: QMainWindow(QWidget parent=None, Qt.WindowFlags flags=0)
            • schrodinger.ui.sketcher.sketcher
          • PyQt4.QtGui.QToolBar: QToolBar(QString, QWidget parent=None) QToolBar(QWidget parent=None)
            • schrodinger.ui.sketcher.sketcherGUIMultiColumnToolBar
          • schrodinger.application.bioluminate.antibody.search_results_table.SplitTable: A widget to contain both split search results tables (i.e.
      • schrodinger.ui.maestroui.SMResidue
      • schrodinger.infra.projectmodel.schrodinger
      • schrodinger.ui.sketcher.sketcherChemicalKnowledge
      • schrodinger.ui.sketcher.sketcherLID
      • schrodinger.ui.sketcher.sketcherMolecule
      • schrodinger.ui.sketcher.sketcherStyle
  • tuple: tuple() -> empty tuple tuple(iterable) -> tuple initialized from iterable's items
    • schrodinger.application.licensing.licadmin.stat_info: stat_info(total, used)
  • 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.systype.TyperBase.__metaclass__
  • schrodinger.utils.csv_unicode.writer: A CSV writer that can handle Unicode characters.
  • xrange: xrange([start,] stop[, step]) -> xrange object
• schrodinger.application.mcpro.zmat.proteinHandler: Class provides methods to write the pepz input file
• PyQt4.QtCore.pyqtWrapperType
• 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.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.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.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.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
  • 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.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.