Class Hierarchy

schrodinger.application.desmond.enhsamp.ASLObject
urllib2.AbstractBasicAuthHandler
- urllib2.ProxyBasicAuthHandler
  - schrodinger.utils.urllib.ProxyBasicAuthHandler
urllib2.AbstractDigestAuthHandler
- urllib2.ProxyDigestAuthHandler
  - schrodinger.utils.urllib.ProxyDigestAuthHandler
schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer: Convert a structure file of screen results (or inputs) into active and decoy fingerprints and report similarity metrics between the fingerprint sets.
schrodinger.test.stu.outcomes.desmond.Adaptive: Class created to define it's base class at runtime.
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.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.assignbondorders.AssignBondOrders
schrodinger.application.desmond.gui_v2.AtomGroupRow
schrodinger.application.desmond.gui.AtomGroupRow
schrodinger.application.desmond.fep_mapping.AtomMappingData: Class to store intermediary and final data structures for atom mapping
schrodinger.application.combiglide.packages.chutils.Attachment: Store information about an attachment point, which is a heavy atom on a structure.
- schrodinger.application.combiglide.packages.chutils.AdductAttachment
- schrodinger.application.combiglide.packages.chutils.SubstrateAttachment
schrodinger.pipeline.pipeutils.BackwardsReader: Read a file line by line, backwards.
schrodinger.application.desmond.fepdiff.BaseBlockProperty
- schrodinger.application.desmond.fepdiff.FEPIOBlockProperty
  - schrodinger.application.desmond.fepdiff.FEPIOAtommapBlockProperty
- schrodinger.application.desmond.fepdiff.FFIOBlockProperty
urllib2.BaseHandler
- urllib2.AbstractHTTPHandler
  - urllib2.HTTPHandler
    - schrodinger.utils.urllib.MyHTTPHandler
  - urllib2.HTTPSHandler
    - schrodinger.utils.urllib.HTTPSHandler
      - schrodinger.utils.urllib.MyHTTPSHandler
- urllib2.ProxyBasicAuthHandler
  - schrodinger.utils.urllib.ProxyBasicAuthHandler
- urllib2.ProxyDigestAuthHandler
  - schrodinger.utils.urllib.ProxyDigestAuthHandler
- urllib2.ProxyHandler
  - schrodinger.utils.urllib.ProxyHandler: A ProxyHandler subclass that loads its proxy configuration from 'web_proxy.json' file in the Schrodinger app data directory.
SocketServer.BaseRequestHandler: Base class for request handler classes.
- SocketServer.StreamRequestHandler: Define self.rfile and self.wfile for stream sockets.
  - BaseHTTPServer.BaseHTTPRequestHandler: HTTP request handler base class.
    - schrodinger.application.glide.http_server.GlideHTTPHandler: This class, derived from BaseHTTPRequestHandler, implements the do_GET and do_POST methods.
SocketServer.BaseServer: Base class for server classes.
- SocketServer.TCPServer: Base class for various socket-based server classes.
  - BaseHTTPServer.HTTPServer
    - schrodinger.application.glide.http_server.GlideHTTPServer: This is a variant on HTTPServer that doesn't shut down requests immediately, but keeps them around until glide_shutdown_request is called.
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.desmond.fepdiff.DihedmapBlockDiffer: A class to compare the difference of dihedral block of two FFIOStructure instance.
- schrodinger.application.desmond.fepdiff.DihedralBlockDiffer: A class to compare the difference of dihedral block of two FFIOStructure instance.
schrodinger.application.desmond.cns_io.CNSData
schrodinger.application.desmond.meta.CV: base class for collective variable
- schrodinger.application.desmond.meta.CVAngle: A class to define angle collective variable.
- schrodinger.application.desmond.meta.CVDihedral: A class to define dihedral collective variable.
- schrodinger.application.desmond.meta.CVDist: distance collective variable
- schrodinger.application.desmond.meta.CVrgyr: Radius of Gyration Collective Variable
- schrodinger.application.desmond.meta.CVrgyr_mass: Radius of Gyration Collective Variable
- schrodinger.application.desmond.meta.CVrmsd: rmsd collective variable
- schrodinger.application.desmond.meta.CVrmsd_symm: rmsd collective variable
- schrodinger.application.desmond.meta.CVwhim: whim collective variable
- schrodinger.application.desmond.meta.CVzdist: This collective variable reports an absolute Z-distance.
- schrodinger.application.desmond.meta.CVzdist0: This collective variable reports an absolute Z-distance from the simulation box origin (Z==0).
schrodinger.protein.captermini.CapTermini
schrodinger.ui.widgettable.CellIterator: column.cell row.cell Class for iterating over cells in a row or column and for getting a cell Cells are indexed starting with 1 Ex: cell = row.cell[1] or: cell = column.cell[1]
schrodinger.application.combiglide.packages.chutils.ChUtils: Utilities generally useful in core-hopping
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.macromodel.utils.ComUtilAppSci: Subclass of ComUtil with defaults that are closer to the current Maestro version.
  - schrodinger.application.macromodel.utils.ComUtil_2010: This class will be deprecated in the next release.
schrodinger.application.glide.poseviewconvert.Complex: A helper class to split a receptor-ligand complex structure into ligand, and receptor structure components, and write the structure components to new files.
schrodinger.ui.qt.appframework.ConfigDialog: Toplevel Qt widget that mimics the Maestro Start dialog.
- schrodinger.ui.qt.appframework.GPGPUConfigDialog: This Config Dialog supports enumerating GPGPU's and allowing the user to select which GPGPU(s) they'd like to use.
  - schrodinger.application.desmond.gui_v2.DesmondGuiConfigDialog: MultiGPGPU dialog with Desmond-specific customization - automatic GPU selection
    - schrodinger.application.desmond.gui_v2.DesmondRestGuiConfigDialog
    - schrodinger.application.desmond.gui_v2.SingleGpuDesmondGuiConfigDialog
  - schrodinger.application.desmond.gui.DesmondGuiConfigDialog: MultiGPGPU dialog with Desmond-specific customization - automatic GPU selection
    - schrodinger.application.desmond.gui.DesmondRestGuiConfigDialog
    - schrodinger.application.desmond.fep_gui.FEPConfigDialog
      - schrodinger.application.desmond.fep_gui.RESTFEPConfigDialog
schrodinger.structutils.rmsd.ConformerRmsd: A class to calculate the root mean square deviatation between the atomic coordinates of two conformer structure.Structure objects.
schrodinger.structutils.rmsd.ConformerRmsdX: A class to calculate the root mean square deviatation between the atomic coordinates of two conformer structure.Structure objects.
schrodinger.application.bioluminate.protein.Consensus: Access the atoms, residues, and molecules (or just their indices) that are considered to be consensus objects for a template structure and query structure.
schrodinger.application.glide.glide.Constraint: Class defining a docking constraint in the receptor.
- schrodinger.application.glide.glide.AcceptorConstraint: H-Bond constraint that was specified as a *receptor* acceptor atom.
- schrodinger.application.glide.glide.DonorConstraint: H-Bond constraint that was specified as a *receptor* donor atom.
- schrodinger.application.glide.glide.HydrophobicConstraint
- schrodinger.application.glide.glide.MetCoordConstraint
- schrodinger.application.glide.glide.MetalConstraint: This constraint was specified as a metal receptor atom.
- schrodinger.application.glide.glide.NOEConstraint
- schrodinger.application.glide.glide.PositionalConstraint
schrodinger.application.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: Class to generate structural classes for a structure containing a single ring system.
schrodinger.utils.ligfilter.Criterion: A base class for a structure matching criterion.
- schrodinger.utils.ligfilter.AslCriterion: This criterion considers a Structure as matching if the stored ASL expresson match returns at least one atom.
- schrodinger.utils.ligfilter.PredefinedCriterion: A structure matching criterion that acts on the value of a predefined function applied to the structure.
- schrodinger.utils.ligfilter.PropertyCriterion: A structure matching criterion that acts on the presence or value of a specific structure property.
- schrodinger.utils.ligfilter.SmartsCriterion: A structure matching criterion that looks for a match to a Definition instance, which is comprised of a collection of SMARTS patterns.
schrodinger.utils.ligfilter.CriterionParser: A class for parsing a general property or predefined matching criterion.
schrodinger.application.mcpro.modelsystemwizard.ModelSystem.CtObj: This class is created to group together all relevant data about a structure and to provide functions for displaying the structure on Maestro workspace easily.
schrodinger.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.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.test.stu.outcomes.desmond.Desmond: General class used for Desmond workups.
schrodinger.application.desmond.system_builder_util.DesmondBoxSize
schrodinger.trajectory.desmondsimulation.DesmondSimulation
- schrodinger.trajectory.desmondsimulation.FepSimulation: A class for handling Fep Simulation
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.infra.mmim.MMIMDict: A class for setting and getting MMIM keyword values.
- schrodinger.infra.mmkv.MMKVSettings: A class for setting and getting MMKV keyword values.
- schrodinger.application.desmond.ffiostructure._ElementProperty: A dictionary of other_block element based properties.
  - schrodinger.application.desmond.ffiostructure._FEPIOElementProperty: hash(x)
  - schrodinger.application.desmond.ffiostructure._FFIOElementProperty: hash(x)
- schrodinger.application.desmond.ffiostructure._FEPIOProperty: A dictionary of fepio properties, with all dict methods.
- schrodinger.application.desmond.ffiostructure._FEPIOSubBlockProperty: A dictionary of fepio sub-block properties.
- schrodinger.trajectory.ffstructure._FFAngleProperty: A dictionary to hold angle force field parameters.
- schrodinger.trajectory.ffstructure._FFBondProperty: A dictionary to hold bond force field parameters.
- schrodinger.trajectory.ffstructure._FFConstraintProperty: A dictionary to hold constraint force field parameters.
- schrodinger.trajectory.ffstructure._FFDihedralProperty: A dictionary to hold dihedral force field parameters.
- schrodinger.trajectory.ffstructure._FFExclusionProperty: A dictionary to hold exclusion pair force field parameters.
- schrodinger.application.desmond.ffiostructure._FFIOProperty: A dictionary of ffio properties, with all dict methods.
- schrodinger.application.desmond.ffiostructure._FFIOSubBlockProperty: A dictionary of ffio sub-block properties.
- schrodinger.trajectory.ffstructure._FFPairProperty: A dictionary to hold pair force field parameters.
- schrodinger.trajectory.ffstructure._FFPseudoProperty: A dictionary to hold pseudo atom force field parameters.
- schrodinger.trajectory.ffstructure._FFRestraintProperty: A dictionary to hold restraint force field parameters.
- schrodinger.trajectory.ffstructure._FFSiteProperty: A dictionary to hold site force field parameters.
- schrodinger.trajectory.ffstructure._FFVdwtypeProperty: A dictionary to hold Van der Waals type force field parameters.
- schrodinger.trajectory.ffstructure._FFVirtualProperty: A dictionary to hold virtual site force field parameters.
- schrodinger.application.qsite.input._GenDict: A dictionary-like class for getting and setting keywords in the &gen section of qsite input, which controls the Jaguar portion of the calculation.
- schrodinger.application.qsite.input._MopacDict: A dictionary-like class for getting and setting keywords in the &mopac section of qsite input, which controls the Jaguar/MOPAC portion of the calculation.
- schrodinger.structure._StructureAtomProperty: A dictionary of atom based properties.
- schrodinger.structure._StructureBondProperty: A dictionary of bond based properties.
- schrodinger.structure._StructureProperty: A dictionary of Structure based properties, with all dict methods.
schrodinger.pipeline.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
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.test.stu.outcomes.desmond.Fep: A Class to help with Demsond's FEP-specifc workup
schrodinger.structutils.smilesfilter.FilterReporter: A class to handle reporting of results from the remove_dupes function.
schrodinger.analysis.enrichment.FingerprintFromFileGenerator: Class to generate (identifier, fingerprint) items, one at a time, from a structure file.
schrodinger.application.lid.lid2d.intervaltree2d.FirstSecondaryStructure
schrodinger.application.prime.primefix.FixForPrime: Wrapper class to house the combination of methods for fixing a structure for Prime.
schrodinger.application.desmond.fep_gui.FragClass: Class for storing the data for each fragment row.
schrodinger.application.desmond.gaussian_filter.GaussianFilter
Tkinter.Grid: Geometry manager Grid.
- Tkinter.Widget: Internal class.
  - Tkinter.Button: Button widget.
    - schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
      - schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
    - schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
  - Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
    - schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
      - schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
  - Tkinter.Checkbutton: Checkbutton widget which is either in on- or off-state.
    - schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
      - schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
    - schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
      - schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
      - schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
  - Tkinter.Entry: Entry widget which allows to display simple text.
    - schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
    - schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
  - Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
    - schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
      - schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
      - schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
      - schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
      - schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
        
        schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
        
        schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
      - schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
      - schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
      - schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
      - schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
      - schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
      - schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
    - schrodinger.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.utils.urllib.ProxyPasswordManager
  - schrodinger.utils.urllib.ProxyPasswordManagerQt: A password manager sub-class that uses Qt to post a dialog to request the password.
optparse.HelpFormatter: Abstract base class for formatting option help.
- optparse.IndentedHelpFormatter: Format help with indented section bodies.
  - schrodinger.utils.cmdline.DelegatingIndentedHelpFormatter: An IndentedHelpFormatter class that allows an Option class to alter its own option string if it has a process_option_strings method.
Tkinter.Image: Base class for images.
- Tkinter.PhotoImage: Widget which can display colored images in GIF, PPM/PGM format.
  - schrodinger.ui.widget.tkinterwidget.PhotoImage: Class that mimics the Tkinter.PhotoImage class.
schrodinger.application.mcpro.read_output.ImportSumfile: Method to read all data from current summary/monitor file and return the status and properties of interest in a hash.
schrodinger.application.desmond.fepdiff.IndexMapper
schrodinger.application.lid.lid2d.intervaltree2d.IntervalTree
schrodinger.application.lid.lid2d.intervaltree2d.IntervalTreeNode
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.job.launcher.Launcher: Run a program (typically a Python or shell script) under job control.
schrodinger.application.lid.ligand_interaction_diagram.LigandInteractionDiagram
schrodinger.application.desmond.mdpose.mdpose_analysis.MDPoseAnalysis
- schrodinger.application.desmond.mdpose.mdpose_analysis.Contact
- schrodinger.application.desmond.mdpose.mdpose_analysis.RMSD
- schrodinger.application.desmond.mdpose.mdpose_analysis.Tanimoto
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.propertyselector.PropertySelectorMenu: Pull-down menu style property selected Used by VSW GUI
  - 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
rfc822.Message: Represents a single RFC 2822-compliant message.
- mimetools.Message: A derived class of rfc822.Message that knows about MIME headers and contains some hooks for decoding encoded and multipart messages.
schrodinger.application.desmond.meta.Meta
schrodinger.application.desmond.meta.MetaDynamicsAnalysis: Analysis tools for Desmond's metadynamics jobs.
Tkinter.Misc: Internal class.
- Tkinter.BaseWidget: Internal class.
  - Tkinter.Toplevel: Toplevel widget, e.g.
    - schrodinger.ui.widget.tkinterwidget.Toplevel: Class that mimics the Tkinter.Toplevel class.
  - Tkinter.Widget: Internal class.
    - Tkinter.Button: Button widget.
      - schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
        
        schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
      - schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
    - Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
      - schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
        
        schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
    - Tkinter.Checkbutton: Checkbutton widget which is either in on- or off-state.
      - schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
        
        schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
      - schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
        
        schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
        
        schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
    - Tkinter.Entry: Entry widget which allows to display simple text.
      - schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
      - schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
    - Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
      - schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
        
        schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
        
        schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
        
        schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
        
        schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
        
        schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
        
        schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
        
        schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
        
        schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
        
        schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
        
        schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
        
        schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
        
        schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
      - schrodinger.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.ui.appframework.AppFramework: The AppFramework class is basically a hull for applications.
schrodinger.trajectory.rmsd2d.ModelBase
- schrodinger.trajectory.rmsd2d.MultiprocessingModel
- schrodinger.trajectory.rmsd2d.ThreadingModel
schrodinger.application.mcpro.modelsystemwizard.ModelSystem: This is where all information regarding the model system are stored.
schrodinger.application.mcpro.modelsystemwizard.ModelSystemPanel: Class to draw the model-system-creation panel
schrodinger.structutils.io.MultiFileReader: Reads structures from multiple files.
schrodinger.structutils.io.MultiFileWriter: Writes structres to basename-NNN<extension> while never writing more than 100,000 structures to a file.
schrodinger.application.desmond.fep_gui.MutClass: Class for storing the data for each mutation row.
schrodinger.application.bioluminate.protein.Mutation: Helper class for Mutator.
schrodinger.application.bioluminate.protein.Mutator: Mutates a set of residues in a protein structure allowing concurrent mutations as well as the option to limit concurrent mutations to sequential residues only.
optparse.Option: Instance attributes: _short_opts : [string] _long_opts : [string]
- schrodinger.utils.cmdline.SingleDashOption: A class to automatically translate long options with single dashes into double dash long options, but still print out help with the single dash.
optparse.OptionContainer: Abstract base class.
- optparse.OptionParser: Class attributes: standard_option_list : [Option] list of standard options that will be accepted by all instances of this parser class (intended to be overridden by subclasses).
  - schrodinger.utils.cmdline.SingleDashOptionParser: An OptionParser subclass that allows long options with a single dash.
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.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
      - schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
      - schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
      - schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
        
        schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
        
        schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
      - schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
      - schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
      - schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
      - schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
      - schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
      - schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
    - schrodinger.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.energygroup.PairDict: PairDict is a special dictionary that treats pairs with the same element as equals, independent of order.
schrodinger.application.mcpro.perturbations.PertID: Storage class for perturbation identification
schrodinger.application.mcpro.perturbations.PertReorder: Storage class for perturbation reordering
schrodinger.application.mcpro.perturbations.Perturbations: Class to read, create, and manipulate the graph of perturbations from which user-specified list of fragments will be converted to a list of FEPs to be run
schrodinger.pipeline.pipeio.PipeIO: Parent class for all Pipeline I/O classes.
- schrodinger.pipeline.pipeio.Grid: A class to hold a set of grid files (compressed or uncompressed).
- schrodinger.pipeline.pipeio.PhaseDB: A class to hold the absolute pathname of a Phase database.
- schrodinger.pipeline.pipeio.Structures: A class to hold the names of structure files.
- schrodinger.pipeline.pipeio.Text: A class to hold the names of one or more text (or log) files.
schrodinger.pipeline.pipeline.Pipeline: A controller responsible for running the stages in the correct order.
Tkinter.Place: Geometry manager Place.
- Tkinter.Widget: Internal class.
  - Tkinter.Button: Button widget.
    - schrodinger.ui.widget.tkinterwidget.Button: Class that mimics the Tkinter.Button class.
      - schrodinger.ui.widgettable.ButtonCell: Subclass of Tkinter Button widget and Cell.
    - schrodinger.ui.widget.tkinterwidget.NoteBookButton: Button Specifically designed for use with the Schoridinger-ized NoteBook Mega-Widget.
  - Tkinter.Canvas: Canvas widget to display graphical elements like lines or text.
    - schrodinger.ui.widget.tkinterwidget.Canvas: Class that mimics the Tkinter.Canvas class.
      - schrodinger.ui.widgettable.CanvasCell: Subclass of Tkinter Canvas widget and Cell.
  - Tkinter.Checkbutton: Checkbutton widget which is either in on- or off-state.
    - schrodinger.ui.widget.tkinterwidget.Checkbutton: Class that mimics the Tkinter.Checkbutton class.
      - schrodinger.ui.widgettable.CheckbuttonCell: Subclass of Tkinter Checkbutton widget and Cell.
    - schrodinger.ui.widget.tkinterwidget.PickToggle: Class meant to replicate Maestro pick toggles.
      - schrodinger.ui.widget.tkinterwidget.PickAtomToggle: Class meant to replicate Maestro atom pick toggles.
      - schrodinger.ui.widget.tkinterwidget.PickBondToggle: Class meant to replicate Maestro bond pick toggles.
  - Tkinter.Entry: Entry widget which allows to display simple text.
    - schrodinger.ui.widget.tkinterwidget.Entry: Class that mimics the Tkinter.Entry class.
    - schrodinger.ui.widget.tkinterwidget.TableEntry: Class of Tkinter.Entry widget intended for use with Schrodinger Table class which is still under development.
  - Tkinter.Frame: Frame widget which may contain other widgets and can have a 3D border.
    - schrodinger.ui.widget.tkinterwidget.Frame: Class that mimics the Tkinter.Frame class.
      - schrodinger.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
      - schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
      - schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
      - schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
        
        schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
        
        schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
      - schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
      - schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
      - schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
      - schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
      - schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
      - schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
    - schrodinger.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_v2.PosResRow
schrodinger.application.desmond.gui.PosResRow
schrodinger.application.glide.glideanalysis.PoseLibrary: A helper class to sort a pose library.
schrodinger.application.bioluminate.protein.PrimeStructure
schrodinger.ui.qt.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
- schrodinger.application.bioluminate.propfilter.PropertySelectorWithRanges: A PropertySelector class that appends ranges to the names of numeric properties.
schrodinger.protein.assignment.ProtAssign
PyQt4.QtCore.QAbstractTableModel
PyQt4.QtGui.QDialog
PyQt4.QtGui.QDialog
PyQt4.QtGui.QFileDialog
PyQt4.QtGui.QWidget
schrodinger.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.trajectory.rmsd2d.RMSDMultiprocessing
- schrodinger.trajectory.rmsd2d.RMSDThreading
schrodinger.ui.qt.rama.Rama: A class showing a matplotlib plot of the Phi and Psi angles in a helix
- schrodinger.application.bioluminate.protein_structure_quality.HomologyRama: A Ramachandran plot customized for the Protein Structure Quality Viewer
schrodinger.ui.rama.Rama
schrodinger.ui.appframework.ReadDialog: Dialog allowing user to specify a file to read in.
schrodinger.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.application.mcpro.residuetools.ResidueTools: Class with tools to help in manipulating proteins
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.combiglide.packages.classification_scheme.Scheme: Class that stores the structure of the classification scheme.
schrodinger.application.lid.lid2d.intervaltree2d.SecondSecondaryStructure
schrodinger.protein.sequence.Sequence: Class representing a sequence of protein residues.
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.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.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.test.stu.outcomes.desmond.SystemBuilder: General class used for system builder workups.
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
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
- UserDict.IterableUserDict
  - schrodinger.pipeline.stage.Stage
    - schrodinger.pipeline.stages.filtering.ChargeFilterStage: Stage-based class for filtering a set of structure files by total charge.
    - schrodinger.pipeline.stages.combine.CombineStage: Stage for combining multiple Structures objects into one.
    - schrodinger.pipeline.stages.macromodel.ConfSearchStage: Stage for running MacroModel calculations
    - schrodinger.pipeline.stages.convert.ConvertStage: Stage for converting structure files from one format to another Each file is converted using Schrodingers specific conversion utility and the number of files is not changed.
    - schrodinger.pipeline.stages.phase.DBConfSitesStage: Stage for generating conformations for structures in a Phase database.
    - schrodinger.pipeline.stages.phase.DBExportStage: Stage for exporting structures from a Phase database.
    - schrodinger.pipeline.stages.phase.DBManageStage: Stage for creating a Phase database.
    - schrodinger.pipeline.stages.glide.DockingStage: VSW stage for performing Glide docking
    - schrodinger.pipeline.stages.filtering.DrugLikeSplitStage: Stage for splitting the input ligand structures into 3 groups:
    - schrodinger.pipeline.stages.example.ExampleStage
    - schrodinger.pipeline.stages.gencodes.GenCodesStage: Stage for generating compound and variant codes, which are stored as properties.
    - schrodinger.pipeline.stages.combine.GenerateCovalentComplexesStage: Stage for combining specified receptor with specified ligands via covalent bond to form complexes.
    - schrodinger.pipeline.stages.filtering.GeneratePropsStage: Ev:85070
    - schrodinger.pipeline.stages.glide.GlideSortStage: Stage for sorting Glide _pv/lib.mae files.
    - schrodinger.pipeline.stages.glide.GridgenStage
    - schrodinger.pipeline.stages.filtering.LigFilterStage: Stage interface for the LigFilter utility.
    - schrodinger.pipeline.stages.ligprep.LigPrepStage: Pipeline stage for running LigPrep on the input structures
    - schrodinger.pipeline.stages.prime.MMGBSAStage: Stage for running Prime MM-GBSA on input structures.
    - schrodinger.pipeline.stages.filtering.MergeDuplicatesStage: Stage for removing duplicate variants within each root (compound) based on unique SMILES strings.
    - schrodinger.pipeline.stages.glide.MergeStage: Stage for merging up to 100 Glide output files with 'glide_ensemble_merge'.
    - schrodinger.pipeline.stages.ligprep.PostLigPrepStage: This stage limits the number of steroisomers, removes states penalized by Epik/Ionizer, and generates the variant codes.
    - schrodinger.pipeline.stages.prime.PrimeStage: Prime Active Site Optimization stage: Performs the familiar sidechain prediction plus minimization, used by IFD jobs.
    - schrodinger.pipeline.stages.pull.PullStage: Stage for extracting a subset of ligands/compounds (and their variants) from a second set of ligand files, given the number or percent to keep from a first set of ligand files.
    - schrodinger.pipeline.stages.qsite.QSiteStage: Stage for running QSite jobs.
    - schrodinger.pipeline.stages.qikprop.QikPropStage: Stage for running QikProp jobs.
    - schrodinger.pipeline.stages.gencodes.RestoreTitlesStage: Stage for copying titles for each input ligand from the 's_pipeline_title_backup' property to the 's_m_title' property.
    - schrodinger.pipeline.stages.rmsd.RmsdStage: Stage for calculating RMSDs for structures in two sets.
    - schrodinger.pipeline.stages.macromodel.SampleRingsStage: Stage for sampling rings with 7 or more members using MacroModel
    - schrodinger.pipeline.stages.semiemp.SemiEmpStage: Stage for running semi-empirical jobs.
    - schrodinger.pipeline.stages.filtering.SubSetStage: Stage for making a subset of the input files based on a list of titles or other property.
schrodinger.application.vsw.vswinput.VSWWriter: Use writeInputFile() method
schrodinger.ui.qt.appframework2.validation.ValidationMixin: This mix-in provides validation functionality to other classes, including the ability to attach external Validators and to designate methods as validation methods, which will be called when the validate method is invoked.
- schrodinger.ui.qt.appframework2.baseapp.ValidatedPanel
  - schrodinger.ui.qt.appframework2.af2.App
    - schrodinger.ui.qt.appframework2.af2.JobApp
      - schrodinger.application.jaguar.gui.base_panel.BasePanel: A base class for all Jaguar GUIs.
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
        
        schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
      - schrodinger.application.matsci.reordergui.ReorderAtomPanel: A simple panel that takes two selected entries and allows one of them to be reordered - this is mainly for testing and example purposes.
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.
    - schrodinger.ui.appframework.AppFramework: The AppFramework class is basically a hull for applications.
- Tkinter.Toplevel: Toplevel widget, e.g.
  - schrodinger.ui.widget.tkinterwidget.Toplevel: Class that mimics the Tkinter.Toplevel class.
schrodinger.ui.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
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.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.combiglide.packages.classification_scheme._Class: A Class in the classification scheme.
schrodinger.application.prepwizard._CommonProblemsFixer: Class for fixing common structure problems.
schrodinger.trajectory.desmondsimulation._DesmondFrame: _DesmondFrame contains simulation data at a particular time.
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.trajectory.ffstructure._FFAngleIterator
schrodinger.trajectory.ffstructure._FFBondIterator
schrodinger.trajectory.ffstructure._FFConstraintIterator
schrodinger.trajectory.ffstructure._FFDihedralIterator
schrodinger.trajectory.ffstructure._FFExclusionIterator
schrodinger.trajectory.ffstructure._FFPairIterator
schrodinger.trajectory.ffstructure._FFPseudoIterator
schrodinger.trajectory.ffstructure._FFRestraintIterator
schrodinger.trajectory.ffstructure._FFSiteIterator
schrodinger.trajectory.ffstructure._FFVdwtypeIterator
schrodinger.trajectory.ffstructure._FFVirtualIterator
schrodinger.trajectory.desmondsimulation._FepTrajectory._FepFrame
schrodinger.trajectory.desmondsimulation._FepTrajectory
schrodinger.application.desmond.energygroup._Group
schrodinger.application.phase.hypothesis._HypothesisFeature: Class representing a hypothesis feature.
schrodinger.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.utils.ligfilter._MySplit
schrodinger.application.combiglide.packages.classification_scheme._Node: A node in the classification scheme.
reportlab.pdfgen.textobject._PDFColorSetter: Abstracts the color setting operations; used in Canvas and Textobject asseumes we have a _code object
- reportlab.pdfgen.canvas.Canvas: This class is the programmer's interface to the PDF file format.
  - schrodinger.application.desmond.report_helper.NumberedCanvas
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.project._SelectedRowsIterator: Iterator for selected rows of the project or group
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.ui.rama.Rama.backbone_dihedral
schrodinger.ui.qt.rama.Rama.backbone_dihedral
schrodinger.protein.assignment.ProtAssign.changeable
- schrodinger.protein.assignment.ProtAssign.amide_changeable
- schrodinger.protein.assignment.ProtAssign.amine_changeable
- schrodinger.protein.assignment.ProtAssign.carboxyl_changeable
- schrodinger.protein.assignment.ProtAssign.histidine_changeable
- schrodinger.protein.assignment.ProtAssign.rotatable_changeable
- schrodinger.protein.assignment.ProtAssign.water_changeable
schrodinger.protein.analysis.Report.data_set.data_point: Class that holds the data for each point in a data set
schrodinger.protein.analysis.Report.data_set: Base class for all data sets.
- schrodinger.protein.analysis.Report.Bfactor_data_set: Class to compute and hold data for B-Factors
- schrodinger.protein.analysis.Report.Gfactor_summary_data_set: Class to compute and hold data for G-factor summaries of the Backbone and Sidechain dihedrals.
- schrodinger.protein.analysis.Report.backbone_dihedral_data_set: Class to compute and hold data for Backbone Dihedrals
- schrodinger.protein.analysis.Report.bond_angle_data_set: Class to compute and hold data for Bond Angle Deviations
- schrodinger.protein.analysis.Report.bond_length_data_set: Class to compute and hold data for Bond Length Deviations
- schrodinger.protein.analysis.Report.chirality_data_set: Class to compute and hold C-alpha chirality data
- schrodinger.protein.analysis.Report.gamma_Bfactor_data_set: Class to compute and hold data for B-Factors of sidechain gamma atoms
- schrodinger.protein.analysis.Report.improper_torsion_data_set: Class to compute and hold RMS data for improper torsions
- schrodinger.protein.analysis.Report.missing_atoms_data_set: Class to compute and hold information on missing atoms
- schrodinger.protein.analysis.Report.peptide_planarity_data_set: Class to compute and hold data for Peptide Planarity
- schrodinger.protein.analysis.Report.sidechain_dihedral_data_set: Class to compute and hold data for Sidechain Dihedrals
- schrodinger.protein.analysis.Report.sidechain_planarity_data_set: Class to compute and hold RMS data for planarity of sidechains
- schrodinger.protein.analysis.Report.steric_clash_data_set: Class to compute and hold data for Steric Clashes.
  - schrodinger.protein.analysis.Report.primex_steric_clash_data_set: A subclass of steric_clash_data_set that computes clashes using a different set of criteria used by PrimeX Polish.
schrodinger.protein.assignment.ProtAssign.hbond_cluster
schrodinger.application.glide.liaison_lsbd.liaison
schrodinger.protein.analysis.Report.local_atom: Private class used to store atom information locally for speed
schrodinger.protein.analysis.Report.local_protein: Private class used to store protein information locally for convenience
schrodinger.protein.analysis.Report.local_residue: Private class used to store residue information locally for convenience
object: The most base type
- schrodinger.application.desmond.title_to_hex.Analysis
- schrodinger.trajectory.analysistool.AnalysisTool: AnalysisTool is a base class for creating analyses of schrodinger.trajectory.desmondsimulation.DesmondSimulation objects.
  - schrodinger.trajectory.analysis.Angle: A tool to calculate angles between selected atom sets.
  - schrodinger.trajectory.analysis.AverageStructure: A tool to calculate average position over time for each atom in a set.
  - schrodinger.trajectory.analysis.CenterOfMass: A tool to calculate center of mass of selected atoms.
  - schrodinger.trajectory.analysis.CenterOfMotion: A tool to calculate center of motion of selected atoms.
  - schrodinger.trajectory.analysis.CovarianceMatrix: A tool to calculate covmatiant matrix.
  - schrodinger.trajectory.analysis.Dihedral: A tool to calculate dihedral angles from selected atom sets.
  - schrodinger.trajectory.analysis.Distance: A tool to calculate distances between selected atom sets.
  - schrodinger.application.desmond.energygroup.EnergyGroup: A tool to calculate group-group interaction.
  - schrodinger.trajectory.analysis.HydrogenBondFinder: A tool to find hydrogen bonds present between two sets of molecules.
  - schrodinger.trajectory.analysis.HydrogenBondTracker: A tool to track the state of hydrogen bonds between atom sets.
  - schrodinger.trajectory.hydrophobiccontactfinder.HydrophobicContactFinder: A tool to find hydrogen bonds present between two sets of molecules.
  - schrodinger.trajectory.jcoupling.Jcoupling: A class to calculate NMR J-coupling, using Karplus' relation.
  - schrodinger.trajectory.analysis.LigandRMSD: A tool to calculate Root Mean Square Deviation from reference positions of a small molecule.
  - schrodinger.trajectory.analysis.MolecularSurfaceArea: A tool to calculate molecular (connolly) surface area.
  - schrodinger.trajectory.analysis.PlanarAngle: A tool calculate inter-planar angles from selected atoms
  - schrodinger.trajectory.analysis.PolarSurfaceArea: A tool to calculate Polar Surface Area.
  - schrodinger.trajectory.analysis.Position: A tool to track positions of atoms.
  - schrodinger.trajectory.protliginteractionfinder.ProtLigInteractionFinder: A tool to find between two selections.
  - schrodinger.trajectory.analysis.RMSD: A tool to calculate Root Mean Square Deviation from reference positions.
  - schrodinger.trajectory.analysis.RMSF: A tool to calculate Root Mean Square Fluctation from reference positions.
  - schrodinger.trajectory.analysis.RadiusOfGyration: A tool to calculate radius of gyration for a set of atoms.
  - schrodinger.trajectory.analysis.Ramachandran: A tool to look at Ramachandran information and plots.
  - schrodinger.trajectory.saltbridgefinder.SaltBridgeFinder: A tool to find hydrogen bonds present between two sets of molecules.
  - schrodinger.trajectory.analysis.SecondaryStructure: A tool to track secondary protein structure.
  - schrodinger.trajectory.analysis.SolventAccessibleSurfaceArea: A class which calculates Solvent Accessible Surface Area.
  - schrodinger.trajectory.analysis.SolventAccessibleSurfaceAreaByResidue: A class which calculates Solvent Accessible Surface Area and returns results groupped by residues.
  - schrodinger.trajectory.analysis.VolumeMapper: A tool to map atomic volume onto a grid.
- schrodinger.application.desmond.simulation_block_data.Array_Prop
- schrodinger.structutils.analyze.AslLigandSearcher: Search a Structure instance for putative ligands with an Atom Selection Language expression.
- schrodinger.application.desmond.cmj.AslValidator
- schrodinger.application.desmond.mdkey.AtomGroup
- schrodinger.application.desmond.cms.AtomGroup
- schrodinger.application.desmond.gui_v2.AtomGroupFrame: Frame for the "Atom group" box of the Misc tab of the Advanced Options dialog.
- requests.auth.AuthBase: Base class that all auth implementations derive from
  - schrodinger.test.stu.client.ApiKeyAuth: An authorization method that uses an api key.
- schrodinger.application.desmond.extend_fep_backend.Backend: The interface, only takes a tgz_fn which contains all files to run the job.
- exceptions.BaseException: Common base class for all exceptions
  - exceptions.Exception: Common base class for all non-exit exceptions.
    - schrodinger.application.desmond.antlr3.exceptions.BacktrackingFailed: @brief Raised to signal failed backtrack attempt
    - schrodinger.application.canvas.similarity.CanvasSimilarityNotImplemented: For CanvasSimilarity method not yet implemented
    - schrodinger.application.desmond.systype.DetectionError
    - schrodinger.application.desmond.systype.FormatError
    - httplib.HTTPException
      - schrodinger.utils.urllib.ProxyTunnelError
    - schrodinger.application.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.output.JaguarParseError
    - schrodinger.application.jaguar.gui.utils.JaguarSettingError: An exception indicating that there was an error with the user-specified Jaguar settings
    - 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.MopacCalculationError
    - 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.structure.UnsupportedOption: An exception class to indicate an attempt to set an option that is not supported.
      - schrodinger.structure.UnsupportedOptionValue: An exception class to indicate an attempt to set an option to a value that is supported.
    - schrodinger.application.desmond.cmj.ParseError
    - schrodinger.utils.urllib.PasswordRetryException
    - schrodinger.project.ProjectException
      - schrodinger.project.ArchivedProjectException
      - schrodinger.project.InvalidProjectException
      - schrodinger.project.InvalidProjectVersion
      - schrodinger.project.LockedProjectException
    - schrodinger.protein.assignment.PropKaException
    - 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.test.stu.outcomes.failures.WorkupFailure: General failure during workup.
        
        schrodinger.test.stu.outcomes.failures.JobFailure: Base class for various problems with test/job execution.
        
        schrodinger.test.stu.outcomes.failures.JobDiedFailure
        
        schrodinger.test.stu.outcomes.failures.JobExpectedFailure
        
        schrodinger.test.stu.outcomes.failures.JobKilledFailure
        
        schrodinger.test.stu.outcomes.failures.JobLaunchFailure
        
        schrodinger.test.stu.outcomes.failures.LicenseFailure
        
        schrodinger.test.stu.outcomes.structure_comparisons._WorkupFailure: Exceptions with lists or dicts of nested differences.
      - 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.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.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.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.impl.TopoException
    - schrodinger.application.desmond.systype.UnknownAppError
    - schrodinger.application.desmond.systype.UnknownRuleError
    - schrodinger.application.lid.ligand_interaction_diagram.UserChooseNothingException
    - 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.application.jaguar.gui.utils.JaguarSettingWarning: A warning indicating that a user-specified Jaguar settings could not be loaded into the GUI
- schrodinger.job.queue.BaseJob: A base job class for jobs run under JobDJ.
  - schrodinger.application.desmond.cmj.JobAdapter: This adapts the `Job' class to the `que.BaseJob' class.
  - schrodinger.job.queue.JobControlJob: This class defines a job control job to be run under JobDJ.
    - schrodinger.application.desmond.mdpose.mdpose_glide.MDPoseGlideJob
    - schrodinger.application.desmond.mdpose.mdpose_strain_energy.MDPoseStrainJob
    - schrodinger.application.matsci.jaguarworkflows.RobustSubmissionJob: A JobControlJob object that will retry to submit multiple times for fizzled, jobs (if the queue setting is such) but will not attempt to retry a job that died.
    - schrodinger.test.stu.run.TestJCJob: Like a normal JobControlJob, but:
  - schrodinger.job.queue.SubprocessJob: A job for running an external process.
    - schrodinger.test.stu.run.TestSPJob: Like a normal SubprocessJob job, but:
  - schrodinger.job.queue.ThreadedJob: This class is for jobs that don't run under job control yet can have significant computational requirements in the python part of the JobDJ process.
- schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer: @brief Common recognizer functionality.
  - schrodinger.application.desmond.antlr3.recognizers.Lexer: @brief Baseclass for generated lexer classes.
    - schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer
  - schrodinger.application.desmond.antlr3.recognizers.Parser: @brief Baseclass for generated parser classes.
    - schrodinger.application.desmond.antlr3.debug.DebugParser
    - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser
  - schrodinger.application.desmond.antlr3.tree.TreeParser: @brief Baseclass for generated tree parsers.
- schrodinger.application.desmond.extend_fep.Baseunit: This contains info common to all work units, they should subclass this unit to get jobname, master_msj, and master_checkpoint_fn, and perturbation_dir
  - schrodinger.application.desmond.extend_fep.Workunit: This subclasses Baseunit and adds attributes specific to the workunit being created.
- schrodinger.application.desmond.simulation_block_test.Block
- schrodinger.application.jaguar.output.BondCharge: A class to store bond-midpoint charges calculated in ESP fitting.
- schrodinger.trajectory.BondRotator.BondRotator: perform RB scan
- schrodinger.application.desmond.ffiostructure.CMSReader: A class for reading structures from a CMS format file.
- schrodinger.application.desmond.envir.CONST
- schrodinger.analysis.enrichment.Calculator: A class to calculate enrichment terms for a screen.
- schrodinger.application.canvas.cluster.CanvasFingerprintCluster: A class which handles clustering of canvas fingerprints.
  - schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI: A subclass of the canvas fingerprint cluster manager which is to be used from a program with a command line interface.
  - schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI: A subclass of the canvas fingerprint clusterer which is to be used from a program with a TKInter interface.
- schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator: A class to encapsulate canvas finger print generation.
  - schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI: A subclass of the canvas fingerprint generator which is to be used from a program with a command line interface.
  - schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI: A subclass of the canvas fingerprint generator which is to be used from a program with a TKInter interface.
- schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity: A class which encapsulates the Canvas fingerprint similarity tools.
  - schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI: A subclass of the CanvasFingerprintSimilarity class which supports operations from the command line.
  - schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI: A subclass of the canvas fingerprint similarity manager which is to be used from a program with a TKInter interface.
- schrodinger.structutils.interactions.pi.CationPiInteraction: The object that stores the data for a Cation-Pi interaction
- schrodinger.structutils.interactions.pi.Centroid: The object that stores data about a centroid
- schrodinger.application.desmond.mdkey.CfgAtom: This class represents the "atomic" parameters in a config file.
- schrodinger.protein.getpdb_utility.Chain: Class to handle splitting a chain out of a PDB file.
- schrodinger.application.matsci.nano.check.CheckInput: Check user input.
  - schrodinger.application.matsci.nano.sheet.CheckInput: Check user input.
  - schrodinger.application.matsci.nano.tube.CheckInput: Check 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.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.application.bioluminate.pml_menus.AutoColorObjects
    - schrodinger.application.bioluminate.pml_menus.AutoColorCarbons
  - schrodinger.application.bioluminate.pml_menus.AutoCycleColor
    - schrodinger.application.bioluminate.pml_menus.AutoCycleCarbonColor
  - schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor
    - schrodinger.application.bioluminate.pml_menus.ColorCalphasByBFactor
  - schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum
    - schrodinger.application.bioluminate.pml_menus.ColorCalphasBySpectrum
    - schrodinger.application.bioluminate.pml_menus.ColorCarbonsBySpectrum
  - schrodinger.application.bioluminate.pml_menus.ColorBySubstructure
  - schrodinger.application.bioluminate.pml_menus.ColorChainbows
  - schrodinger.application.bioluminate.pml_menus.ColorChains
    - schrodinger.application.bioluminate.pml_menus.ColorChainsByCalpha
    - schrodinger.application.bioluminate.pml_menus.ColorChainsByCarbon
  - schrodinger.application.bioluminate.pml_menus.CustomColor
  - unreachable.CustomRecentColor
- 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.nano.constants.Constants: Collect constants.
- schrodinger.application.desmond.cms.Constraint
- _abcoll.Container
  - _abcoll.Sequence: All the operations on a read-only sequence.
    - _abcoll.MutableSequence
      - UserList.UserList
        
        schrodinger.structutils.sort.DsuList: A class to sort a list with special behaviors.
- schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateData: This class is a base class for constraint and scan coordinate classes.
  - schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateData: This class stores all data for a single constraint coordinate.
  - schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData: This class stores all data for a single scan coordinate.
- schrodinger.application.desmond.util.Counter: This class was originally designed for the convenience of gridding widgets.
- schrodinger.infra.util.CreateWhenNeeded: This class can be used like property() (i.e., it is a descriptor; see section 3.3.2.2 in the python reference).
- schrodinger.application.qsite.input.Cut: A class to handle representation and printing of general qm region cuts.
- schrodinger.application.desmond.config.DEFAULT_SETTING
- schrodinger.application.desmond.antlr3.dfa.DFA: @brief A DFA implemented as a set of transition tables.
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1
  - schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24
  - schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25
- schrodinger.application.desmond.antlr3.dottreegen.DOTTreeGenerator: A utility class to generate DOT diagrams (graphviz) from arbitrary trees.
- schrodinger.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.infra.mmerr.disable_mmerr: Turn off mmerr reporting within a context or while a function is being run.
  - 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.jaguar.output.Dipole: A class for storing dipole information.
- schrodinger.structutils.measure.DistanceCellIterator: Iterate through neighbors of specified atoms.
- schrodinger.ui.qt.swidgets.EnforcingValidatorMixin: This is a mixin class to be added to a QValidator subclass.
  - schrodinger.application.matsci.atomicsymbolsgui.ElementValidator: A QValidator to check if the input is a partial or valid atomic symbol.
- schrodinger.application.desmond.cmj.Engine
- schrodinger.application.glide.ensemble_selection.Ensemble: Objects of this class are basically dumb "structs" that hold the basic attributes of a specific ensemble.
- schrodinger.application.desmond.gui_v2.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.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.replica_sid_generator.FEPReport
- schrodinger.application.desmond.fep_reporter.FEPReportMaker
- schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport
- schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro
- schrodinger.application.bioluminate.pml_menus.FakeMaestro
- schrodinger.application.glide.glide.FeaturePattern: Class defining a constraint feature pattern.
- schrodinger.application.desmond.mdkey.FepSchedule
- schrodinger.structure.FormatReader: This is a base class for all file format readers.
  - schrodinger.structure.MaestroReader: A class for reading structures from a Maestro (M2io) format file.
    - schrodinger.structure.MaestroReaderWithPositions: A class for rapid random access to the structures in a Maestro file.
  - schrodinger.structure.Mol2Reader: A class for reading structures from a mol2 format file.
  - schrodinger.structure.PDBReader: A class for reading structures from a PDB format file.
  - schrodinger.structure.SDReader: A class for reading structures from a SD format file.
- logging.Formatter: Formatter instances are used to convert a LogRecord to text.
  - schrodinger.application.matsci.textlogger.GetLogger.MyFormatter: Extend logging.Formatter to customize the formats of different log levels and to textwrap the messages.
- 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.trajectory.atomselection.FrameAslSelection: A class for selecting atoms from frames in a given simulation using ASL.
- schrodinger.trajectory.atomselection.FrameIndexSelection: A class that defines a static set of indices to be selected from all frames.
- schrodinger.trajectory.atomselection.FrameSliceSelection: A class for efficiently selecting a range of atoms.
- schrodinger.application.bioluminate.antibody_utils.FrameworkTemplate
- schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate
- schrodinger.application.desmond.fepana.FreeEnergyContrib
- schrodinger.application.jaguar.output.FukuiIndices: A class to store Atomic Fukui indices.
- schrodinger.application.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.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.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.multisimstartup.Help
- schrodinger.application.desmond.config._FepSchedule.Helper
- 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_cache.HuntCache: A HuntCache object represents a particular "hunt cache" a file that stores hunt results for re-use.
- schrodinger.application.qsite.input.HydrogenCap: A class to handle representation and printing of hydrogen caps for the qm region.
- schrodinger.application.phase.hypothesis.Hypothesis
- schrodinger.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.job.jobcontrol._JobInitializer: A class to handle class initialization and termination.
- schrodinger.application.desmond.gui_v2.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.ExcitedStateValidatorMixin: A mixin that verifies that there are no input structures with spin multiplicity greater than one when excited state toggle is set in theory tab.
    - schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
  - schrodinger.application.jaguar.gui.base_panel.PropertiesValidatorMixin: A mixin that verifies that all selected properties can be calculated for the input entries.
    - schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
- schrodinger.application.jaguar.gui.base_panel.InputTabMixin: A mixin for panels that use the Input tab.
  - schrodinger.application.jaguar.gui.base_panel.InputTabJobMixin: A mixin for panels that use the Input tab and launch "standard" Jaguar jobs (i.e.
    - schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
- schrodinger.application.desmond.antlr3.streams.IntStream: @brief Base interface for streams of integer values.
  - schrodinger.application.desmond.antlr3.streams.CharStream: @brief A source of characters for an ANTLR lexer.
    - schrodinger.application.desmond.antlr3.streams.ANTLRStringStream: @brief CharStream that pull data from a unicode string.
      - schrodinger.application.desmond.antlr3.streams.ANTLRFileStream: @brief CharStream that opens a file to read the data.
      - schrodinger.application.desmond.antlr3.streams.ANTLRInputStream: @brief CharStream that reads data from a file-like object.
  - schrodinger.application.desmond.antlr3.streams.TokenStream: @brief A stream of tokens accessing tokens from a TokenSource
    - schrodinger.application.desmond.antlr3.streams.CommonTokenStream: @brief The most common stream of tokens
      - schrodinger.application.desmond.antlr3.streams.TokenRewriteStream: @brief CommonTokenStream that can be modified.
    - schrodinger.application.desmond.antlr3.debug.DebugTokenStream
  - schrodinger.application.desmond.antlr3.tree.TreeNodeStream: @brief A stream of tree nodes
    - schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream: @brief A buffered stream of tree nodes.
- schrodinger.application.bioluminate.pml_menus.InterfaceMixin: Determine the Protein-Protein interface atoms
  - schrodinger.application.bioluminate.pml_menus.GenerateInterfaceSelection
  - schrodinger.application.bioluminate.pml_menus.InterfacePreset
- schrodinger.application.ligprep.ionizer.Ionizer: Class for ionizing structures (part of LigPrep).
- _abcoll.Iterable
  - _abcoll.Sequence: All the operations on a read-only sequence.
    - _abcoll.MutableSequence
      - UserList.UserList
        
        schrodinger.structutils.sort.DsuList: A class to sort a list with special behaviors.
- schrodinger.application.jaguar.output.JaguarAtomicResults: A class for holding atomic level properties.
- schrodinger.application.jaguar.input.JaguarInput: A class for specifying Jaguar input.
- schrodinger.application.jaguar.output.JaguarOptions: A class for keeping track of specific calculation options.
- schrodinger.application.jaguar.output.JaguarOutput: A class for accessing Jaguar output properties.
  - schrodinger.application.qsite.output.QSiteOutput: A class to hold output information from a QSite run.
- schrodinger.application.jaguar.output.JaguarResults: A class for holding results for a specific geometry.
  - schrodinger.application.qsite.output.QSiteResults: A class for holding results for a specific geometry.
- schrodinger.application.desmond.cmj.Job
  - schrodinger.application.desmond.stage.AnalysisJob
    - schrodinger.application.desmond.stage.SeaJob
    - schrodinger.application.desmond.stage.TimeSeriesAnalysisJob
  - schrodinger.application.desmond.stage.DesmondJob
    - schrodinger.application.desmond.stage.FepJob
    - schrodinger.application.desmond.stage.FepanaJob
  - schrodinger.application.desmond.stage.MetadynamicsAnalysisJob
  - schrodinger.application.desmond.stage.WaterMapAnaJob
- schrodinger.job.jobcontrol.Job: A class to access a specific record in the job database.
- schrodinger.job.queue.JobDJ: Class for running commands/jobs in parallel under jobcontrol.
  - schrodinger.test.stu.run.TestQueue: Like a normal JobDJ, but:
- 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.ui.appframework.MultiInputParams: A class to hold the state of the MultiInputFrame and set up files needed by backend calculations.
- schrodinger.application.desmond.cmj.JobOutput
  - schrodinger.application.desmond.cmj.JobInput
- schrodinger.application.desmond.cmj.JobStatus
- schrodinger.application.desmond.mdkey.Key
- schrodinger.infra.licensing.License
- schrodinger.utils.license.License: Class to allow easy licensing of Python scripts
- schrodinger.application.matsci.buildcomplex.Ligand: Stores information about a ligand structure
- schrodinger.structutils.analyze.Ligand: A putative AslLigandSearcher ligand structure with read-only data and convenience methods.
- schrodinger.application.bioluminate.pml_menus.LigandActionMixin: Class that contains a method to restrict the asl to Ligands only
  - schrodinger.application.bioluminate.pml_menus.ExcludeOrganicFromSelection
  - schrodinger.application.bioluminate.pml_menus.GenerateLigandSelection
  - schrodinger.application.bioluminate.pml_menus.PresetAction: Base class for Preset Actions
    - schrodinger.application.bioluminate.pml_menus.AntibodyPreset
    - schrodinger.application.bioluminate.pml_menus.BAndSPreset
    - schrodinger.application.bioluminate.pml_menus.BFactorPreset
    - schrodinger.application.bioluminate.pml_menus.DefaultPreset
    - schrodinger.application.bioluminate.pml_menus.InterfacePreset
    - schrodinger.application.bioluminate.pml_menus.LigandPreset
    - schrodinger.application.bioluminate.pml_menus.PrettyPubPreset: Show the object as nice-looking cartoon ribbons
    - schrodinger.application.bioluminate.pml_menus.SimplePreset
    - schrodinger.application.bioluminate.pml_menus.TechnicalPreset
  - schrodinger.application.bioluminate.pml_menus.RestrictToOrganic
  - schrodinger.application.bioluminate.pml_menus.ShowLigandLines
  - schrodinger.application.bioluminate.pml_menus.ShowLigandSpheres
  - schrodinger.application.bioluminate.pml_menus.ShowLigandTubes
- schrodinger.application.desmond.covalent_fep_prep.LigandGenerator: Will generate a list of ligands preped for a mapper job
- schrodinger.application.desmond.replica_sid_generator.LigandReport
- schrodinger.job.queue.LinkedList: A doubly linked list, providing constant time addition, size, and truth checks.
  - schrodinger.job.queue.RunningJobs: A LinkedList subclass that tracks running jobs and keeps a tally of jobs running on each machine.
- schrodinger.job.queue.LinkedListNode: A node for the LinkedList class, holding a value, and a reference to the previous and next node in the list.
- schrodinger.infra.mmkv.MMKVArgList: A class to provide list-like access to MMKV/MMIM array properties.
  - schrodinger.infra.mmim.MMIMArgList
- schrodinger.structure.MaestroTextReader: A class for reading structures from a Maestro format file.
- schrodinger.maestro.markers.Marker: Class to manipulate a set of markers in the Workspace by ASLs.
- schrodinger.application.jaguar.gui.base_panel.MarkerMixin: A mixin for panels that want markers displayed only when certain tabs are active.
  - schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin: A mixin for marking constraints from the Scan or Optimization tabs.
    - schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin: A mixin that receives updates from Scan and Optimization tabs when new coordinate is added.
    - schrodinger.application.jaguar.gui.base_panel.OptimizationTabMarkerMixin: A mixin for marking constraints from the Optimization tab
      - schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin: A mixin for panels that contain a MultiStructureTab and an Optimization Tab.
        
        schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
    - schrodinger.application.jaguar.gui.base_panel.ScanTabMarkerMixin: A mixin for marking constraints from the Scan tab
- schrodinger.ui.qt.appframework2.markers.MarkerMixin: A mixin for adding markers and controlling their visibility.
  - schrodinger.ui.qt.appframework2.af2.App
    - schrodinger.ui.qt.appframework2.af2.JobApp
      - schrodinger.application.jaguar.gui.base_panel.BasePanel: A base class for all Jaguar GUIs.
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
        
        schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
      - schrodinger.application.matsci.reordergui.ReorderAtomPanel: A simple panel that takes two selected entries and allows one of them to be reordered - this is mainly for testing and example purposes.
- schrodinger.application.desmond.measurement.Measurement: Basic method for uncertainty propagation: Say we have a few measurements: x1, x2, x3, ..., and they each has a uncertainty: d1, d2, d3, ..., respectively.
- schrodinger.application.desmond.enhsamp.Meta
- schrodinger.structutils.minimize.Minimizer: A class to provide force field energy and minimization.
- schrodinger.infra.mmobject.MmObject: An abstraction of the bookkeeping needed to create a garbage collected MM object.
  - schrodinger.infra.mmbitset.Bitset: This class represents a bitset, with each element either 1 or 0.
  - schrodinger.application.jaguar.mmjag.MmJag: A reference counting class for dealing with mmjag handles.
  - schrodinger.project.Project: Class to handle Maestro Projects.
  - schrodinger.infra.table.Table: Class to handle mmtables.
  - schrodinger.infra.mmlist.mmlist: Wrap an anderlying mmlist "instance" and provides access to its members through the python sequence syntax.
- schrodinger.utils.moduleproxy.ModuleProxy: A class to use as a placeholder for a non-essential module, raising an exception when something tries to use it.
- schrodinger.application.moldescriptors.impl.MolecularDescriptorsOptions: A class to provide various options that can be passed to calculate molecular descriptors.
- schrodinger.application.mopac.MopacCalculation: A class for running MOPAC calculations.
- schrodinger.application.mopac.MopacResults: A class to store MOPAC results.
- schrodinger.structure.MultiFileStructureReader: Provides a single iterator that reads structure from multiple files.
- schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin: A mixin for panels that contain a MultiStructureTab.
  - schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin: A mixin for panels that contain a MultiStructureTab and an Optimization Tab.
    - schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
- schrodinger.application.matsci.nano.tube.MultiWalledNanoTube: Build a multi-walled nanotube by assembling specific NanoTubes.
- 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.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.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
    - schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
- schrodinger.application.desmond.enhsamp.Node
  - schrodinger.application.desmond.enhsamp.Bind
  - schrodinger.application.desmond.enhsamp.FcnCall
  - schrodinger.application.desmond.enhsamp.If
  - schrodinger.application.desmond.enhsamp.Iter
  - schrodinger.application.desmond.enhsamp.Let
  - schrodinger.application.desmond.enhsamp.Lit
  - schrodinger.application.desmond.enhsamp.Series
  - schrodinger.application.desmond.enhsamp.String
  - schrodinger.application.desmond.enhsamp.Var
- schrodinger.application.desmond.reorder_atom.Node
- schrodinger.application.jaguar.output.NormalMode: A class for storing normal mode results.
- schrodinger.application.jaguar.output.Orbital: A class for storing orbital information.
- schrodinger.structure.PDBWriter: A class for writing PDB-formatted files.
- schrodinger.structutils.interactions.pi.PiPiInteraction: The object that stores the data for a Pi-Pi interaction
- schrodinger.application.desmond.picklejar.Picklable
  - schrodinger.application.desmond.stage.FepJob
  - schrodinger.application.desmond.stage.FepanaJob
  - schrodinger.application.desmond.cmj.StageBase
    - schrodinger.application.desmond.stage.AlignCore
    - schrodinger.application.desmond.stage.Analysis
    - schrodinger.application.desmond.stage.AssignForcefield
    - schrodinger.application.desmond.stage.BuildGeometry
    - schrodinger.application.desmond.stage.CalcDdg
    - schrodinger.application.desmond.stage.Concluder: This stage does not create any jobs for the 'cmj.QUEUE'.
    - schrodinger.application.desmond.stage.CovMapper
    - schrodinger.application.desmond.stage.DesmondExtend
    - schrodinger.application.desmond.stage.Extern
    - schrodinger.application.desmond.stage.FepAnalysis
      - schrodinger.application.desmond.stage.FepAnalysis2
    - schrodinger.application.desmond.stage.FepMapper
    - schrodinger.application.desmond.stage.FepMapperReport
    - schrodinger.application.desmond.stage.FepMapping
    - schrodinger.application.desmond.stage.ForcefieldBuilder
    - schrodinger.application.desmond.stage.McproStageBase
      - schrodinger.application.desmond.stage.McproSimulate
      - schrodinger.application.desmond.stage.McproSystemBuilder
    - schrodinger.application.desmond.stage.Multisim
    - schrodinger.application.desmond.stage.PLAnalysis: This class sets up and runs automatic analsyis for protein-ligand complex
    - schrodinger.application.desmond.stage.Primer
    - schrodinger.application.desmond.stage.Simulate
      - schrodinger.application.desmond.stage.FepVrun
      - schrodinger.application.desmond.stage.Minimize
      - schrodinger.application.desmond.stage.ReplicaExchange
        
        schrodinger.application.desmond.stage.LambdaHopping
      - schrodinger.application.desmond.stage.Vrun
    - schrodinger.application.desmond.stage.SolvatePocket
    - schrodinger.application.desmond.stage.Stop
    - schrodinger.application.desmond.stage.SystemBuilder
    - schrodinger.application.desmond.stage.Task
    - schrodinger.application.desmond.stage.Trajectory
    - schrodinger.application.desmond.stage.Trim
    - schrodinger.application.desmond.stage.WaterMap
    - schrodinger.application.desmond.stage.WaterMapCluster
    - schrodinger.application.desmond.stage.WaterMapPostAnalysis
- schrodinger.application.desmond.picklejar.PickleJar
- schrodinger.application.desmond.picklejar.PickleState
- schrodinger.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.utils.preferences.Preferences: A class that allows Pythonic access to the mmpref library.
- schrodinger.application.desmond.covalent_fep_prep.PrepLigand
- schrodinger.graphics3d.common.Primitive: All 3D objects derive from this class.
  - schrodinger.graphics3d.arrow.ArrowCore: Base class for drawing a 3D arrow
    - schrodinger.graphics3d.arrow.Arrow: Class for drawing a 3D arrow in OpenGL.
    - schrodinger.graphics3d.arrow.MaestroArrow: Class for creating a 3D arrow in Maestro
  - schrodinger.graphics3d.box.Box: Class to draw a 3D box in OpenGL.
  - schrodinger.graphics3d.lines.Lines: Class to draw a set of lines in OpenGL.
  - schrodinger.graphics3d.polygon.Polygon: Class to draw a flat polygon in OpenGL.
  - schrodinger.graphics3d.polyhedron.Polyhedron: Class to draw a 3D polyhedron with OpenGL using the current context in whatever is the current drawable (which could be Maestro).
    - schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore
      - schrodinger.graphics3d.polyhedron.MaestroCube: Class to draw a 3D cube in Maestro's Workspace.
        
        schrodinger.graphics3d.polyhedron.Cube: This class is now deprecated.
      - schrodinger.graphics3d.polyhedron.MaestroDodecahedron: Class to draw a 3D dodecahedron in Maestro's Workspace.
        
        schrodinger.graphics3d.polyhedron.Dodecahedron: This class is now deprecated.
      - schrodinger.graphics3d.polyhedron.MaestroIcosahedron: Class to draw a 3D icosahedron in Maestro's Workspace.
        
        schrodinger.graphics3d.polyhedron.Icosahedron: This class is now deprecated.
      - schrodinger.graphics3d.polyhedron.MaestroOctahedron: Class to draw a 3D octahedron in Maestro's Workspace.
        
        schrodinger.graphics3d.polyhedron.Octahedron: This class is now deprecated.
      - schrodinger.graphics3d.polyhedron.MaestroTetrahedron: Class to draw a 3D tetrahedron in Maestro's Workspace.
        
        schrodinger.graphics3d.polyhedron.Tetrahedron: This class is now deprecated.
  - schrodinger.graphics3d.quadrilateral.Quadrilateral: Class to draw a 3D quadrilateral in OpenGL.
  - schrodinger.graphics3d.sphere.SphereCore: Base class for Sphere and MaestroSphere classes.
    - schrodinger.graphics3d.sphere.MaestroSphere: Class to create a 3D sphere in Maestro.
    - schrodinger.graphics3d.sphere.Sphere: Class to draw a 3D sphere in OpenGL.
- schrodinger.job.queue.PriorityQueue: This is a general priority queue.
- multiprocessing.process.Process: Process objects represent activity that is run in a separate process
  - schrodinger.trajectory.rmsd2d.RMSDMultiprocessing
- schrodinger.application.desmond.covalent_fep_prep.ProcessLigands: Supports calling mapper and generating mae files for running multisim
- schrodinger.application.desmond.covalent_fep_prep.ProcessProteins: The idea here is to use the mapping generated from the ligands to generate mae's for the complex.
- schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry: A class for accessing data about a project table row and the associated structure
  - schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka
- schrodinger.project.ProjectRow: ProjectRow allows access to the structure and properties of an entry in the project.
  - schrodinger.utils.pymol.RowProxy: Proxy for project table row to attach additional data.
- 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.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
  - schrodinger.application.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
    - schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
- schrodinger.application.bioluminate.protein.PropertyCalculator: Class for calculating properties of proteins and protein residues.
- schrodinger.structure.PropertyName: The PropertyName class can be used to display the "user-readable" version of an entry or atom property to the user.
- schrodinger.application.desmond.fep_protein_prep.ProteinPrep: This object will be used to prepare a protein for fep
- 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.utils.pymol.PymolScriptInstance: Represents a PyMOL script for deferred execution.
- schrodinger.application.qsite.input.QMRegion: A class to provide access to a &qmregion specification and the ability to create one on the fly.
- schrodinger.application.qsite.input.QSiteInput
- schrodinger.application.desmond.cmj.Queue
- schrodinger.application.jaguar.gui.base_panel.ReadEditMixin: A mixin for panels that should include Read...
  - schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
  - schrodinger.application.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
    - schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
- 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_v2.RelaxFrame: Frame that includes the "Relax model..." check box and the relaxation protocol entry field.
- schrodinger.application.desmond.stage.Reporter
- schrodinger.job.queue.RequirementsJob: This is a base class that indicates a job has special requirements (e.g.
  - schrodinger.job.queue.LocalhostJob: This class should be used as a mixin on a job type that requires jobs to be run on localhost.
    - schrodinger.job.queue.SubprocessJob: A job for running an external process.
      - schrodinger.test.stu.run.TestSPJob: Like a normal SubprocessJob job, but:
- 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.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.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.structutils.interactions.salt_bridge.SaltBridgeFinder: Find salt-bridge interactions.
- schrodinger.application.jaguar.scan.Scan: A class for storing information about geometry scan variables.
- schrodinger.application.jaguar.output.ScfIteration: A simple storage class for storing info on an SCF iteration.
- schrodinger.utils.sea.Sea: This is the base class the 'Atom', 'List', and 'Map' classes.
  - schrodinger.utils.sea.Atom: This class represents the "atomic" parameters in a config file.
    - schrodinger.utils.sea.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.jaguar.gui.input_tab_widgets.SelectedEntriesColumns: Column constants for the selected entries table
- schrodinger.application.jaguar.gui.input_tab_widgets_hb.SelectedEntriesColumnsHB: Column constants for the HB input tab entries table.
- schrodinger.application.jaguar.gui.input_tab_widgets_pka.SelectedEntriesColumnsPka: Column constants for the pKa selected entries table
- schrodinger.application.desmond.covalent_fep_prep.SetupFEPJob
- schrodinger.application.desmond.gui_v2.SimOptionsFrame: Responsible for drawing the simulation options widgets, including Simulation time and Recording intervals.
- schrodinger.application.desmond.cms.Site
- _abcoll.Sized
  - _abcoll.Sequence: All the operations on a read-only sequence.
    - _abcoll.MutableSequence
      - UserList.UserList
        
        schrodinger.structutils.sort.DsuList: A class to sort a list with special behaviors.
- schrodinger.application.bioluminate.sliderchart.SlidableLine: A line on a matplotlib plot that can be grabbed and moved by the user
  - schrodinger.application.bioluminate.sliderchart.SlidableHLine: A horizontal line on a matplotlib plot that can be grabbed and moved by the user
  - schrodinger.application.bioluminate.sliderchart.SlidableVLine: A vertical line on a matplotlib plot that can be grabbed and moved by the user
- schrodinger.structure.SmilesCsvReader: A class for reading structures from a SMILES CSV formatted file.
- schrodinger.structure.SmilesReader: A class for reading structures from a SMILES formatted file.
- schrodinger.structure.SmilesStructure: SMILES representation of a Structure that is returned by SmilesReader and SmilesCsvReader.
- schrodinger.application.ligprep.ionizer.Spec: This class represents a specification line in the ionizer data file.
- 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.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
  - schrodinger.application.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
    - schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
- schrodinger.ui.appframework.StartDialogParams: A collection of parameter values from the StartDialog class.
- schrodinger.application.desmond.multisimstartup.Startup
- schrodinger.application.matsci.jaguarworkflows.Step: Manages the start, monitoring and finish of a single step in a workflow
  - schrodinger.application.matsci.jaguarworkflows.FrozenStep: A step that does not perform geometry optimization but just runs a calculation at the geometry of the parent step.
  - schrodinger.application.matsci.jaguarworkflows.OptStep: A step that performs a geometry optimization
- 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.bioluminate.propfilter.BooleanDatabaseCriterion
  - schrodinger.application.bioluminate.propfilter.NumericalDatabaseCriterion
- schrodinger.structutils.structalign.StructAlign: This is the class used to perform the structural alignment.
- schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator: A class which generates Structural Interaction Fingerprints.
- schrodinger.application.desmond.stage.FepAnalysis.Structure
- schrodinger.structure.Structure: A general chemical structure object, which may contain multiple molecules.
  - schrodinger.application.desmond.cms.Cms
  - schrodinger.trajectory.cmsstructure.CmsStructure: CmsStructure represents a complete description of Desmond model system, which includes one full ct and several component cts.
  - schrodinger.application.desmond.ffiostructure.FFIOStructure: Class to create python interface to force field data.
  - schrodinger.structure.TextualStructure: A sub-class of Structure for use when reading from a Maestro format file and only the structure-level properties are needed.
- schrodinger.structure.StructureReader: A class to read structures from files of various types.
- schrodinger.structure.StructureWriter: A class for efficient writing of multiple structures to a single structure file.
- schrodinger.trajectory.analysis.Superimposer
- schrodinger.infra.mmsurf.SwigDoubleVector
- schrodinger.infra.mmgpgpu.SwigDoubleVector
- schrodinger.infra.mmgpgpu.SwigDoubleVector3
- schrodinger.infra.mmsurf.SwigDoubleVector3
- schrodinger.infra.mmsurf.SwigIntIntPair
- schrodinger.infra.mmgpgpu.SwigIntIntPair
- schrodinger.infra.mmgpgpu.SwigIntVector
- schrodinger.infra.mmsurf.SwigIntVector
- schrodinger.infra.mmsurf.SwigPyIterator
- schrodinger.trajectory.rdf_backend.SwigPyIterator
- schrodinger.utils.mmutil.SwigPyIterator
- schrodinger.infra.mmgpgpu.SwigPyIterator
- schrodinger.infra.mmsurf.SwigStringVector
- schrodinger.infra.mmgpgpu.SwigStringVector
- schrodinger.infra.mmsurf.SwigUInt64Vector
- schrodinger.infra.mmgpgpu.SwigUInt64Vector
- schrodinger.infra.mmgpgpu.SwigUnsignedIntVector
- schrodinger.infra.mmsurf.SwigUnsignedIntVector
- schrodinger.infra.mmsurf.SwigUnsignedIntVector2
- schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2
- schrodinger.infra.mmsurf.SwigVectorIntIntPair
- schrodinger.infra.mmgpgpu.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.desmond.fep_protein_prep.Tagger
- 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
- unittest.case.TestCase: A class whose instances are single test cases.
  - schrodinger.test.custom_assertions.StructureAssertionsTestCase: "Convenience" class to allow structural assertions to be called similarly to built in assertions.
    - schrodinger.test.custom_test_classes.StructureTestCase: A unit test class that reads in a structure.
- schrodinger.test.stu.run.TestJob: Interface for the TestJCJob and TestSPJob classes
  - schrodinger.test.stu.run.TestJCJob: Like a normal JobControlJob, but:
  - schrodinger.test.stu.run.TestSPJob: Like a normal SubprocessJob job, but:
- 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.jaguar.output.TextParser: A parser to create a JaguarOutput object from a Jaguar output file.
  - schrodinger.application.qsite.output.QSiteTextParser: A subclass of the Jaguar output text parser that adds QSite specific parsing.
- schrodinger.application.jaguar.output.ThermoCollection: A class to store a full set of calculated thermodynamic properties at a given temperature.
- schrodinger.application.jaguar.output.ThermoProp: A class to store the components of calculated thermodynamic properties.
- schrodinger.application.desmond.cmj.Job.Time
- schrodinger.application.desmond.antlr3.tokens.Token: @brief Abstract token baseclass.
  - schrodinger.application.desmond.antlr3.tokens.ClassicToken: @brief Alternative token implementation.
  - schrodinger.application.desmond.antlr3.tokens.CommonToken: @brief Basic token implementation.
- schrodinger.application.desmond.antlr3.recognizers.TokenSource: @brief Abstract baseclass for token producers.
  - schrodinger.application.desmond.antlr3.recognizers.Lexer: @brief Baseclass for generated lexer classes.
    - schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer
- schrodinger.application.desmond.antlr3.tree.Tree: @brief Abstract baseclass for tree nodes.
  - schrodinger.application.desmond.antlr3.tree.BaseTree: @brief A generic tree implementation with no payload.
    - schrodinger.application.desmond.antlr3.tree.CommonTree: @brief A tree node that is wrapper for a Token object.
      - schrodinger.application.desmond.antlr3.tree.CommonErrorNode: A node representing erroneous token range in token stream
      - schrodinger.application.desmond.antlr3.treewizard.TreePattern: When using %label:TOKENNAME in a tree for parse(), we must track the label.
        
        schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern
- schrodinger.application.desmond.antlr3.tree.TreeAdaptor: @brief Abstract baseclass for tree adaptors.
  - schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor: @brief A TreeAdaptor that works with any Tree implementation.
    - schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor: @brief A TreeAdaptor that works with any Tree implementation.
      - schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor: This adaptor creates TreePattern objects for use during scan()
  - schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor: A TreeAdaptor proxy that fires debugging events to a DebugEventListener delegate and uses the TreeAdaptor delegate to do the actual work.
- schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer
- schrodinger.application.desmond.antlr3.treewizard.TreePatternParser
- schrodinger.application.desmond.antlr3.tree.TreeVisitor: Do a depth first walk of a tree, applying pre() and post() actions we go.
- schrodinger.application.desmond.antlr3.treewizard.TreeWizard: Build and navigate trees with this object.
- schrodinger.application.desmond.systype.TyperBase
  - schrodinger.application.desmond.systype.DesmondTyper
  - schrodinger.application.desmond.systype.McproTyper
  - schrodinger.application.desmond.systype.WatermapTyper
- schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_constraints_ui.Ui_Dialog
- schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog
- schrodinger.application.lid.lid_savedialog_ui.Ui_Dialog
- schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_collection_viewer_ui.Ui_Dialog
- schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui.Ui_Dialog
- schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog
- schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog
- schrodinger.application.jaguar.gui.ui.reaction_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.molecule_top_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.output_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.theory_tab_ui.Ui_Form
- schrodinger.application.lid.ligand_interaction_diagram_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.scan_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.irc_bottom_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.transition_state_top_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui.Ui_Form
- schrodinger.application.desmond.input_group_ui.Ui_Form
- schrodinger.application.desmond.rest_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.solvent_tab_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.properties_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.scf_tab_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui.Ui_Form
- schrodinger.application.bioluminate.propfilter_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.input_top_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.multi_structures_ui.Ui_Form
- schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.input_std_bottom_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui.Ui_Form
- schrodinger.ui.ligfilter_ui.Ui_Form
- schrodinger.application.jaguar.gui.ui.molecule_std_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.jaguar.gui.ui.excited_state_widget_ui.Ui_Widget
- schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_ui.Ui_Widget
- schrodinger.application.jaguar.gui.ui.spin_restricted_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.utils.pymol.VisRecord: Represents a surface entry in a "vis_list" file
  - schrodinger.utils.pymol.VisRecordVol: Represents a volume 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.extend_fep.Workflow: Here we assume the user launches the workflow from the top level directory of a mapper job.
  - schrodinger.application.desmond.extend_fep.ExtensionWorkflow
  - schrodinger.application.desmond.extend_fep.RestartWorkflow: This class will create a workflow for running restart jobs
- schrodinger.application.desmond.covalent_fep_prep.Workflow
- schrodinger.application.desmond.fep_protein_prep.Workflow: Will take a list of proteins and a mutation dictionary and return a set of "lig" "rec" legs and msj for running the sims.
- 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.
- argparse._ActionsContainer
  - argparse.ArgumentParser: Object for parsing command line strings into Python objects.
    - schrodinger.test.stu.base_executable.TestRunnerParser: Subclass that allows easy adding of options.
- schrodinger.structure._AtomBondContainer: The class to provide access to _StructureBond instances for each bond of an atom.
- schrodinger.application.desmond.gui._AtomGroup: Represents the data of the atom group table? Of the Misc tab of the Advanced Options dialog
- schrodinger.application.desmond.gui_v2._AtomGroup: Represents the data of the atom group table? Of the Misc tab of the Advanced Options dialog
- schrodinger.structure._AtomIterator: Iterates over each _StructureAtom in a _Molecule, _Chain, _Residue or _Ring.
- schrodinger.trajectory.atomselection._AtomSelection: A general class for ASL expression support.
- schrodinger.application.jaguar.output._Attribute: A small utility class to automate and regularize handling of attributes.
- argparse._AttributeHolder: Abstract base class that provides __repr__.
  - argparse.Action: Information about how to convert command line strings to Python objects.
    - schrodinger.test.stu.base_executable.store_server: Argparse action to monkeypatch the server address.
  - argparse.ArgumentParser: Object for parsing command line strings into Python objects.
    - schrodinger.test.stu.base_executable.TestRunnerParser: Subclass that allows easy adding of options.
- schrodinger.job.jobcontrol._Backend: An interface to mmjobbe.
  - schrodinger.application.desmond.meta._Backend
- schrodinger.application.desmond.gui_v2._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
  - schrodinger.application.desmond.gui_v2.MdcAdvancedDialog: Advanced Options dialog for Mdc Desmond panels
  - schrodinger.application.desmond.gui_v2.MinAdvancedDialog: Advanced Minimization options dialog for Desmond panels
- schrodinger.test.stu.client._BaseClient: Base client class providing some reasonable defaults.
  - schrodinger.test.stu.client.TestClient: Interact with the Test server.
- schrodinger.application.desmond.gui_v2._BaseGroup: Inherited by MdGroup and MinimizeGroup, so therefore by all Simulation frames
  - schrodinger.application.desmond.gui_v2.MdGroup: Molecular Dynamics group
- schrodinger.maestro.markers._BaseMarker: Base class for the marker classes.
- schrodinger.structure._BaseWriter: This class provides a common implementation for structure writers.
  - schrodinger.structure.MaestroWriter: A class for more efficient appending of a large number of structures to a single maestro structure file.
  - schrodinger.structure.Mol2Writer: Mol2 support for the StructureWriter class.
  - schrodinger.structure.SDWriter: A class for more efficient appending of a large number of structures to a single SD structure file.
  - schrodinger.structure.SmilesCsvWriter: A class for more efficient writing of a large number of structures to a single SMILES CSV file.
  - schrodinger.structure.SmilesWriter: A class for more efficient writing of a large number of structures to a single SMILES file.
- schrodinger.application.desmond.mdkey._Bool
- schrodinger.structure._Chain: A class used to return chain information when iterating over chains in a Structure object.
- schrodinger.ui.widgettable._Column: Base class for a column
  - schrodinger.ui.widgettable.ButtonColumn: Class defining a column of Buttons
  - schrodinger.ui.widgettable.CanvasColumn: Class defining a column of Canvas objects
  - schrodinger.ui.widgettable.CheckbuttonColumn: Class defining a column of checkbuttons
  - schrodinger.ui.widgettable.EntryFieldColumn: Class defining a column of EntryField cells
  - schrodinger.ui.widgettable.LabelColumn: Class defining a column of Labels
  - schrodinger.ui.widgettable.OptionMenuColumn: Class defining a column of OptionMenuCells.
  - schrodinger.ui.widgettable.RadiobuttonColumn: Class defining a column of Radiobuttons
- schrodinger.structutils.measure._DistanceCell
- schrodinger._DummyMaestroModule: Used to replace schrodinger.maestro.maestro when running outside of Maestro.
- schrodinger.application.desmond.ffiostructure._Element
  - schrodinger.application.desmond.ffiostructure._FEPIOElement: hash(x)
  - schrodinger.application.desmond.ffiostructure._FFIOElement: hash(x)
- schrodinger.application.desmond.mdkey._Evalor
- schrodinger.utils.sea._Evalor: This is the evaluator class for checking validity of parameters.
- schrodinger.application.desmond.ffiostructure._FEPIO: A class to make access of fepio block pythonic.
- schrodinger.application.desmond.ffiostructure._FEPIOSubBlock: A class to make access of fepio sub-block properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FEPIOAngleMap: hash(x)
  - schrodinger.application.desmond.ffiostructure._FEPIOAtomMap: hash(x)
  - schrodinger.application.desmond.ffiostructure._FEPIOBondMap: hash(x)
  - schrodinger.application.desmond.ffiostructure._FEPIODihedMap: hash(x)
  - schrodinger.application.desmond.ffiostructure._FEPIOExclMap: hash(x)
  - schrodinger.application.desmond.ffiostructure._FEPIOPairMap: hash(x)
- schrodinger.application.desmond.ffiostructure._FEPIOSubBlockContainer
  - schrodinger.application.desmond.ffiostructure._FEPIOAngleMapContainer
  - schrodinger.application.desmond.ffiostructure._FEPIOAtomMapContainer
  - schrodinger.application.desmond.ffiostructure._FEPIOBondMapContainer
  - schrodinger.application.desmond.ffiostructure._FEPIODihedMapContainer
  - schrodinger.application.desmond.ffiostructure._FEPIOExclMapContainer
  - schrodinger.application.desmond.ffiostructure._FEPIOPairMapContainer
- schrodinger.trajectory.ffstructure._FFAngle: A class to hold force field parameters for an angle.
- schrodinger.trajectory.ffstructure._FFBond: A class to hold force field parameters for a bond.
- schrodinger.trajectory.ffstructure._FFConstraint: A class to hold force field parameters for a constraint.
- schrodinger.trajectory.ffstructure._FFDihedral: A class to hold force field parameters for a dihedral.
- schrodinger.trajectory.ffstructure._FFExclusion: A class to hold force field parameters for an exclusion pair.
- schrodinger.application.desmond.ffiostructure._FFIO: A class to make access of ffio block pythonic.
- schrodinger.application.desmond.ffiostructure._FFIOSubBlock: A class to make access of ffio sub-block properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOAngle: A class to make access of mmffio angle properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOAngleFBHW: A class to make access of mmffio angle flat bottom properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOBond: A class to make access of mmffio bond properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOConstraint: A class to make access of mmffio constraint properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIODihedral: A class to make access of mmffio dihedral properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOExclusion: A class to make access of mmffio exclusion properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOImproperFBHW: A class to make access of mmffio improper flat bottom properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOPair: A class to make access of mmffio pair properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOPosFBHW: A class to make access of mmffio position flat bottom properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOPseudo: A class to make access of mmffio pseudo properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIORestraint: A class to make access of mmffio restraint properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOSite: A class to make access of mmffio site properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOStretchFBHW: A class to make access of mmffio stretch flat bottom properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOVdwtype: A class to make access of mmffio vdwtype properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOVdwtypescombined: A class to make access of mmffio vdwtype properties more pythonic.
  - schrodinger.application.desmond.ffiostructure._FFIOVirtual: A class to make access of mmffio virtual properties more pythonic.
- schrodinger.application.desmond.ffiostructure._FFIOSubBlockContainer
  - schrodinger.application.desmond.ffiostructure._FFIOAngleContainer
  - schrodinger.application.desmond.ffiostructure._FFIOAngleFBHWContainer
  - schrodinger.application.desmond.ffiostructure._FFIOBondContainer
  - schrodinger.application.desmond.ffiostructure._FFIOConstraintContainer
  - schrodinger.application.desmond.ffiostructure._FFIODihedralContainer
  - schrodinger.application.desmond.ffiostructure._FFIOExclusionContainer
  - schrodinger.application.desmond.ffiostructure._FFIOImproperFBHWContainer
  - schrodinger.application.desmond.ffiostructure._FFIOPairContainer
  - schrodinger.application.desmond.ffiostructure._FFIOPosFBHWContainer
  - schrodinger.application.desmond.ffiostructure._FFIOPseudoContainer
  - schrodinger.application.desmond.ffiostructure._FFIORestraintContainer
  - schrodinger.application.desmond.ffiostructure._FFIOSiteContainer
  - schrodinger.application.desmond.ffiostructure._FFIOStretchFBHWContainer
  - schrodinger.application.desmond.ffiostructure._FFIOVdwtypeContainer
  - schrodinger.application.desmond.ffiostructure._FFIOVdwtypescombinedContainer
  - schrodinger.application.desmond.ffiostructure._FFIOVirtualContainer
- schrodinger.trajectory.ffstructure._FFPair: A class to hold force field parameters for a pair.
- schrodinger.trajectory.ffstructure._FFPseudo: A class to hold force field parameters for a pseudo atom.
- schrodinger.trajectory.ffstructure._FFRestraint: A class to hold force field parameters for a restraint.
- schrodinger.trajectory.ffstructure._FFSite: A class to hold force field parameters for a site.
- schrodinger.trajectory.ffstructure._FFVdwtype: A class to hold force field parameters for a Van der Waals type.
- schrodinger.trajectory.ffstructure._FFVirtual: A class to hold force field parameters for a virtual site.
- schrodinger.test.stu.sysinfo._FakeLocal: The local host.
- schrodinger.test.stu.sysinfo._FakeRemote: The 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._MMVol: The _MMVol class acts as a wrapper around low-level MMVol objects.
- schrodinger.application.desmond.antlr3.main._Main
- schrodinger.application.desmond.gui_v2._MdcBase: The Advanced options dialogs and their tab widgets subclass this class.
  - schrodinger.application.desmond.gui_v2.EnsembleTab: Frame for the Ensemble tab of the Advanced Options dialog.
  - schrodinger.application.desmond.gui_v2.IntegrationTab: Frame for the Integration tab of the Mdc Advanced Options dialogs
  - schrodinger.application.desmond.gui_v2.InteractionTab: Frame for the Interaction frame of the Advanced Options dialog.
  - schrodinger.application.desmond.gui_v2.MdcMiscTab: Frame for the Misc tab of Mdc Advanced Options dialogs.
    - schrodinger.application.desmond.gui_v2.MinMiscTab: Frame for the Misc Tab of Advanced Options dialog of Minimization GUI.
  - schrodinger.application.desmond.gui_v2.MinOutputFrame: Group box "Output" of the "Minimization" tab of Advanced Options dialog.
  - schrodinger.application.desmond.gui_v2.MinimizationTab: Frame for the Minimization tab of the Advanced Options dialog.
  - schrodinger.application.desmond.gui_v2.MinimizerFrame: Group box "Minimizer" of the "Minimization" tab of Advanced Options dialog.
  - schrodinger.application.desmond.gui_v2.OutputTab: Frame for the Output tab of the Advanced Options dialog
  - schrodinger.application.desmond.gui_v2.RandVelFrame: Frame for the "Randomize velocities" group of the Misc tab of Advanced dialog.
  - schrodinger.application.desmond.gui_v2.RestraintsTab: Frame for the Restraints tab of the Advanced Options dialog
- schrodinger.application.desmond.gui._MdcBase: The Advanced options dialogs and their tab widgets subclass this class.
  - schrodinger.application.desmond.gui.EnsembleTab: Frame for the Ensemble tab of the Advanced Options dialog.
  - schrodinger.application.desmond.gui.IntegrationTab: Frame for the Integration tab of the Mdc Advanced Options dialogs
  - schrodinger.application.desmond.gui.MdcMiscTab: Frame for the Misc tab of Mdc Advanced Options dialogs.
    - schrodinger.application.desmond.gui.MinMiscTab: Frame for the Misc Tab of Advanced Options dialog of Minimization GUI.
  - schrodinger.application.desmond.gui.MinimizationTab: Frame for the Minimization tab of the Advanced Options dialog.
  - schrodinger.application.desmond.gui.RestraintsTab: Frame for the Restraints tab of the Advanced Options dialog
  - schrodinger.application.desmond.gui._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
    - schrodinger.application.desmond.gui.MdcAdvancedDialog: Advanced Options dialog for Mdc Desmond panels
    - schrodinger.application.desmond.gui.MinAdvancedDialog: Advanced Minimization options dialog for Desmond panels
- schrodinger.structure._Molecule: A class used to return molecule information when iterating over molecules in a Structure object.
- schrodinger.job.queue._MultiJobFinalizer: A class to allow specification of a function to be invoked when the final job of a group completes successfully.
- schrodinger.structutils.createfragments._Options: A class to hold a list of options.
- schrodinger.application.desmond.ffiostructure._OtherBlock
  - schrodinger.application.desmond.ffiostructure._FEPIOOtherBlock: hash(x)
  - schrodinger.application.desmond.ffiostructure._FFIOOtherBlock: hash(x)
- schrodinger.application.desmond.ffiostructure._OtherBlockContainer: The class to provide access to other block instances.
  - schrodinger.application.desmond.ffiostructure._FEPIOOtherBlockContainer
  - schrodinger.application.desmond.ffiostructure._FFIOOtherBlockContainer
- schrodinger.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.trajectory.analysis._RamachandranCallback: This class implements a callback to print information about selected Ramachandran plot points.
- schrodinger.structure._Residue: A class which is returned by the ResidueIterator and contains information about the residue including the atoms which make it up.
- schrodinger.structure._ResidueIterator: Residue iterator.
- schrodinger.structure._Ring: Class representing a ring.
- schrodinger.structure._RingEdgeIterator: Iterates over edges(bonds) of a _Ring.
- schrodinger.protein.rotamers._Rotamer: A single instance of a rotamer - represents a set of CHI angle values
- schrodinger.protein.rotamers._RotamerIterator: Container for the rotamers which are associated with a particular residue type
- schrodinger.ui.widgettable._Row: Row of a table
- schrodinger.application.ska._SkaData: Data structure for named backend return values...
- schrodinger.structure._StructureAtom: A class to make access of mmct atoms properties more pythonic.
- schrodinger.structure._StructureAtomContainer: The class to provide access to _StructureAtom instances.
- schrodinger.structure._StructureBond: A class for pythonic access to bond properties.
- schrodinger.structure._StructureBondContainer: The class to provide access to _StructureBond instances for each bond in the structure.
- schrodinger.structure._StructureChainIterator: Class for iterating over chains in a Structure.
- schrodinger.structure._StructureDeleter: A resource cleanup class for a single Structure.
- schrodinger.structutils.createfragments._StructureFragmenter: Class to create fragments from a given set of _Options and a given schrodinger.structure.Structure.
- schrodinger.structure._StructureManager: A class to handle Structure life-cycle events: initialization, termination, and deletion.
- schrodinger.structure._StructureMoleculeIterator: Iterates over _Molecule in a Structure.
- schrodinger.structure._StructureRingIterator: Container for all rings in the Structure.
- 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.
- threading._Verbose
  - threading.Thread
    - schrodinger.trajectory.rmsd2d.FrameLoader: A multi-threading class to load trajectory frame.
    - schrodinger.trajectory.rmsd2d.RMSDThreading
- schrodinger.application.desmond.cmj._create_param_when_needed
- schrodinger.application.desmond.config._create_when_needed
- schrodinger.application.desmond.envir._create_when_needed
- 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.application.jaguar.output.CaseInsensitiveString: A class that behaves like a regular string except that comparisons are done on a case insensitive basis.
    - schrodinger.utils.sea.Key: An instance of this class will be used as the key of the Map class (see below).
- schrodinger.application.desmond.enhsamp.binding
- 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
    - schrodinger.application.desmond.fepdiff.TupleDict: A dictionary class that has a tuple as its key.
      - schrodinger.application.desmond.fepdiff.BiDirDualTupleDict: A dictionary class that uses tuple of tuple as its key which treats the inner tuple and its reversed counterpart the same.
      - schrodinger.application.desmond.fepdiff.BiDirTupleDict: A dictionary class that uses tuple as its key which treats the tuple and its reversed counterpart the same.
      - schrodinger.application.desmond.fepdiff.ConstraintTupleDict: A dictionary class that uses tuple as its key.
      - schrodinger.application.desmond.fepdiff.ImproperDualTupleDict: ImproperDualTupleDict use two element tuple of tuple as it key.
      - schrodinger.application.desmond.fepdiff.ImproperTupleDict: A dictionary class that uses tuple as its key.
      - schrodinger.application.desmond.fepdiff.LooseOrderTupleDict: A dictionary class that uses tuple as its key which does not care about the actual order of individual element of the tuple.
  - collections.OrderedDict: Dictionary that remembers insertion order
    - schrodinger.application.bioluminate.protein.OrderedResidueDict: Creates an ordered dictionary for residues in a structure
  - schrodinger.project.PropertyDictionary: A dictionary of properties which can be indexed by dataname or column name (the name visible in the project).
  - configobj.Section: A dictionary-like object that represents a section in a config file.
    - configobj.ConfigObj: An object to read, create, and write config files.
      - schrodinger.application.inputconfig.InputConfig: Parse keyword-value input files and make the settings available in a dictionary-like fashion.
        
        schrodinger.application.glide.glide.GlideJob: Class for writing Glide input files - either Gridgen or Docking.
        
        schrodinger.application.glide.glide.Dock: Class for generating Glide docking input files.
        
        schrodinger.application.glide.glide.Gridgen: Class for writing Glide Grid Generation input files.
        
        schrodinger.application.prime.input.Prime: Class for reading and writing simplified Prime input files.
        
        schrodinger.application.bioluminate.protein.PrimeConfig: Class containing the methods to write Prime input files.
        
        schrodinger.application.macromodel.input._MacroModel: Class for reading and writing simplified MacroModel input files.
        
        schrodinger.application.macromodel.input.ConfSearch: A special class for dealing with Conformation Search jobs.
        
        schrodinger.application.macromodel.input.EmbraceConfSearch: A special class for dealing with Embrace Conformation Search jobs.
        
        schrodinger.application.macromodel.input.EmbraceMinimization: A special class for dealing with Enbrace Minimization jobs.
        
        schrodinger.application.macromodel.input.EnergyListing: A special class for dealing with Energy Listing jobs.
        
        schrodinger.application.macromodel.input.Minimization: A special class for dealing with Minimization jobs.
        
        schrodinger.application.macromodel.input.Minta: A special class for dealing with Minta jobs.
        
        schrodinger.application.macromodel.input.RCE: A special class for dealing with RCE jobs.
  - schrodinger.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.QFileDialog.AcceptMode
  - PyQt4.QtGui.QAction.ActionEvent
  - PyQt4.QtGui.QAbstractSpinBox.ButtonSymbols
  - PyQt4.QtGui.QMovie.CacheMode
  - PyQt4.QtGui.QGraphicsItem.CacheMode
  - PyQt4.QtGui.QGraphicsView.CacheModeFlag
  - PyQt4.QtGui.QAbstractSpinBox.CorrectionMode
  - PyQt4.QtGui.QAbstractItemView.CursorAction
  - PyQt4.QtGui.QDialog.DialogCode
  - PyQt4.QtGui.QFileDialog.DialogLabel
  - PyQt4.QtGui.QMainWindow.DockOption
  - PyQt4.QtGui.QDockWidget.DockWidgetFeature
  - PyQt4.QtGui.QAbstractItemView.DragDropMode
  - PyQt4.QtGui.QGraphicsView.DragMode
  - PyQt4.QtGui.QAbstractItemView.DropIndicatorPosition
  - PyQt4.QtGui.QLineEdit.EchoMode
  - PyQt4.QtGui.QAbstractItemView.EditTrigger
  - PyQt4.QtGui.QAbstractItemDelegate.EndEditHint
  - PyQt4.QtGui.QFileDialog.FileMode
  - PyQt4.QtGui.QListView.Flow
  - PyQt4.QtGui.QGraphicsItem.GraphicsItemChange
  - PyQt4.QtGui.QGraphicsItem.GraphicsItemFlag
  - PyQt4.QtGui.QComboBox.InsertPolicy
  - PyQt4.QtGui.QGraphicsScene.ItemIndexMethod
  - PyQt4.QtGui.QListView.LayoutMode
  - PyQt4.QtGui.QAction.MenuRole
  - PyQt4.QtGui.QListView.Movement
  - PyQt4.QtGui.QMovie.MovieState
  - PyQt4.QtGui.QGraphicsView.OptimizationFlag
  - PyQt4.QtGui.QFileDialog.Option
  - PyQt4.QtGui.QPaintDevice.PaintDeviceMetric
  - PyQt4.QtGui.QGraphicsItem.PanelModality
  - PyQt4.QtGui.QAction.Priority
  - PyQt4.QtGui.QWidget.RenderFlag
  - PyQt4.QtGui.QListView.ResizeMode
  - 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.QComboBox.SizeAdjustPolicy
  - PyQt4.QtGui.QAction.SoftKeyRole
  - PyQt4.QtGui.QAbstractItemView.State
  - PyQt4.QtGui.QValidator.State
  - PyQt4.QtGui.QAbstractSpinBox.StepEnabledFlag
  - PyQt4.QtGui.QFrame.StyleMask
  - PyQt4.QtGui.QFileDialog.ViewMode
  - PyQt4.QtGui.QListView.ViewMode
  - PyQt4.QtGui.QGraphicsView.ViewportAnchor
  - PyQt4.QtGui.QGraphicsView.ViewportUpdateMode
  - schrodinger.ui.sketcher.sketcherMouseAction
- schrodinger.infra.mmsurf.istream
  - schrodinger.infra.mmsurf.ifstream
- schrodinger.infra.mmgpgpu.istream
  - schrodinger.infra.mmgpgpu.ifstream
- schrodinger.application.jaguar.output.line_enumerate: A simple wrapper class to keep track of the line iteration count.
- list: list() -> new empty list list(iterable) -> new list initialized from iterable's items
  - schrodinger.utils.sea.List: This class represents the "list" parameters in a config file.
  - schrodinger.application.desmond.mdkey.List
- schrodinger.infra.mmgpgpu.ostream
  - schrodinger.infra.mmgpgpu.ofstream
    - schrodinger.infra.mmgpgpu.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
  - schrodinger.infra.mmsurf.ofstream
    - schrodinger.infra.mmsurf.TemporaryOFStream: A subclass of ofstream that uses the tempfile module to get a temporary filename and automatically deletes itself at garbage collection.
- 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.QDockWidget.DockWidgetFeatures: QDockWidget.DockWidgetFeatures(QDockWidget.DockWidgetFeatures) QDockWidget.DockWidgetFeatures(int) QDockWidget.DockWidgetFeatures()
  - PyQt4.QtGui.QAbstractItemView.EditTriggers: QAbstractItemView.EditTriggers(QAbstractItemView.EditTriggers) QAbstractItemView.EditTriggers(int) QAbstractItemView.EditTriggers()
  - PyQt4.QtGui.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.QFileDialog.Options: QFileDialog.Options(QFileDialog.Options) QFileDialog.Options(int) QFileDialog.Options()
  - PyQt4.QtGui.QPaintDevice: QPaintDevice()
    - PyQt4.QtGui.QWidget: QWidget(QWidget parent=None, Qt.WindowFlags flags=0)
      - schrodinger.application.desmond.gui.AdvOptionsFrame: Frame for the "Advanced Options" button.
      - schrodinger.ui.qt.appframework2.baseapp.BasePanel
        
        schrodinger.ui.qt.appframework2.baseapp.ValidatedPanel
        
        schrodinger.ui.qt.appframework2.af2.App
        
        schrodinger.ui.qt.appframework2.af2.JobApp
        
        schrodinger.application.jaguar.gui.base_panel.BasePanel: A base class for all Jaguar GUIs.
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
        
        schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
        
        schrodinger.application.matsci.reordergui.ReorderAtomPanel: A simple panel that takes two selected entries and allows one of them to be reordered - this is mainly for testing and example purposes.
      - schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab: The base class for all Jaguar tabs.
        
        schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab: A parent class for the Scan and Optimization tabs
        
        schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab
        
        schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase: A tab for specifying settings for the structures currently selected in the project table.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTab: An input tab that allows the user to specify basis sets.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB: An input tab that is used with Hydrogen Bond task.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka: An input tab that allows the user to specify pKa atoms.
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase: The base class for all molecule tabs.
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab: The standard molecule tab
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector: A Molecule tab that does not use the input selector
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka: The molecule tab used in the PKA panel
        
        schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab: A parent class for tabs that allow transition state, reactant, and product structures to be selected.
        
        schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab
        
        schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab
        
        schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab: Output tab for the Jaguar panels.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabIGO
        
        schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab: " The Molecules tab used in the Reactions panel.
        
        schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab
        
        schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab
        
        schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab: This is the basic SCF tab that is used for majority of tasks.
        
        schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals: This tab is used for SPE and Optimizations tasks and includes the "Use consistent orbital sets when all input structures are isomers" check box
        
        schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabIGO: This tab is used for 'Initial Guess Only' task.
        
        schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab: The Solvent tab using in the pKa panel
        
        schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab: The Solvation tab, which includes solvent model and gas-phase reference energy
        
        schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab: A tab for selecting the level of theory.
        
        schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization: This tab is used for 'Optimization' task.
      - schrodinger.application.jaguar.gui.basis_selector.BasisSelector: A widget for selecting a Jaguar basis set.
        
        schrodinger.application.jaguar.gui.basis_selector._BasisSelectorPopUp: The pop up window that is displayed adjacent to BasisSelectorLineEdit
      - schrodinger.application.moldescriptors.gui.DescriptorsUI
      - schrodinger.application.desmond.gui.EnsembleClassFrame: Frame that includes the Ensemble class pull-down menu and the entry fields correspondint to it.
      - schrodinger.application.desmond.gui.EnsembleTab: Frame for the Ensemble tab of the Advanced Options dialog.
      - schrodinger.application.desmond.cwidget.EntryField: A special composite widget which contains a labeled line edit field.
      - schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget: This widget allows user to specify 'Excited state' options.
        
        schrodinger.application.jaguar.gui.theory_tab_widgets.HFExcitedStateWidget: This widget differs from the parent only by some text, which is specific to HF theory level.
      - schrodinger.application.desmond.cwidget.FileEntry: Class combining a QLabel, QLineEdit, and a QPushButton (Browse...).
      - schrodinger.application.bioluminate.antibody.search_results_table.FullTable: A widget to contain the full search results table
      - schrodinger.application.desmond.fep_gui.HelpLabel: A special composite widget which contains 2 help labels.
      - schrodinger.application.bioluminate.bwidgets.ImportWidget
      - schrodinger.application.desmond.gui.IntegrationTab: Frame for the Integration tab of the Mdc Advanced Options dialogs
      - schrodinger.application.desmond.gui.InteractionTab: Frame for the Interaction frame of the Advanced Options dialog.
      - schrodinger.ui.ligfilter.LigfilterFrame: Frame for setting up Ligfilter jobs, including property/SMARTS criteria and new definitions.
      - schrodinger.application.desmond.gui.MdcMiscTab: Frame for the Misc tab of Mdc Advanced Options dialogs.
        
        schrodinger.application.desmond.gui.MinMiscTab: Frame for the Misc Tab of Advanced Options dialog of Minimization GUI.
      - schrodinger.application.desmond.gui.MinimizationTab: Frame for the Minimization tab of the Advanced Options dialog.
      - schrodinger.application.moldescriptors.gui.MopacUI
      - schrodinger.application.desmond.gui.OutputTab: Frame for the Output tab of the Advanced Options dialog
      - schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin: A mixin for tabs that allow the user to select a basis set.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTab: An input tab that allows the user to specify basis sets.
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab: The standard molecule tab
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector: A Molecule tab that does not use the input selector
        
        schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab: A parent class for tabs that allow transition state, reactant, and product structures to be selected.
        
        schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab
        
        schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab
      - PyQt4.QtGui.QAbstractButton: QAbstractButton(QWidget parent=None)
        
        PyQt4.QtGui.QCheckBox: QCheckBox(QWidget parent=None) QCheckBox(QString, QWidget parent=None)
        
        schrodinger.application.desmond.fep_gui.PickAtomToggle: Pick atom widget with a precommand feature.
        
        schrodinger.application.desmond.fep_gui.PickBondToggle: Pick bond widget with a precommand feature.
        
        schrodinger.application.jaguar.gui.utils.WorkspaceInclusionCheckBox: A checkbox that is skinned to look like the Project Table workspace inclusion checkbox.
        
        PyQt4.QtGui.QPushButton: QPushButton(QWidget parent=None) QPushButton(QString, QWidget parent=None) QPushButton(QIcon, QString, QWidget parent=None)
        
        schrodinger.application.bioluminate.bwidgets.QuickHelpButton: A help button that has a blue gradient
      - PyQt4.QtGui.QAbstractSpinBox: QAbstractSpinBox(QWidget parent=None)
        
        PyQt4.QtGui.QSpinBox: QSpinBox(QWidget parent=None)
        
        schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox: A spin box that allows the empty string as an acceptable value
      - PyQt4.QtGui.QComboBox: QComboBox(QWidget parent=None)
        
        schrodinger.ui.qt.utils.EnhancedComboBox: A combo box with several Pythonic enhancements
        
        schrodinger.application.jaguar.gui.utils.EnhancedComboBox: A combo box for use in the Jaguar GUI with several Pythonic enhancements
        
        schrodinger.application.desmond.fep_gui.MultiSelectComboBox
      - PyQt4.QtGui.QDialog: QDialog(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog: Modal dialog window that allows users to set active databases.
        
        schrodinger.ui.ligfilter.AddDefinitionDialog: Frame for generating a pattern definition.
        
        schrodinger.ui.chooseligand.ChooseLigandDialog
        
        schrodinger.application.bioluminate.pml_menus.ColorChooserPanel: A window that lets the user choose a Maestro color.
        
        schrodinger.application.jaguar.gui.base_panel.CoordinateDialog: This dialog allows user to select corrective action when the same coordinate is found in the lists of scans and constraints.
        
        schrodinger.ui.ligfilter.DefinitionViewerDialog: Frame containing a text box with a text display of the definition.
        
        schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog: A dialog for showing exceptions to users
        
        schrodinger.application.bioluminate.propfilter.PropFilterDialog: Panel to allow the user to define criteria for filtering property values
        
        PyQt4.QtGui.QFileDialog: QFileDialog(QWidget, Qt.WindowFlags) QFileDialog(QWidget parent=None, QString caption=QString(), QString directory=QString(), QString filter=QString())
        
        schrodinger.ui.qt.filedialog.FileDialog: File browser dialog with custom sidebar.
        
        schrodinger.application.jaguar.gui.filedialog.FileDialogWithExtraCombo: A Qt file dialog with an extra combo box about the filename text edit
        
        schrodinger.application.jaguar.gui.filedialog.ReadFileDialog: An Open dialog both with an extra combo box to specify whether "Geometry and settings" or "Geometry only" should be read from the specified file.
        
        schrodinger.application.jaguar.gui.filedialog.WriteFileDialog: A Save dialog both with an extra combo box to specify whether an input or a batch file should be written.
        
        schrodinger.application.bioluminate.bwidgets.SequenceFileDialog: Custom class to handle opening files related to sequences.
        
        schrodinger.application.bioluminate.bwidgets.TemplateFileDialog: File dialog specific to templates
        
        schrodinger.application.jaguar.gui.filedialog.WriteFileDialogNoBat: A Save dialog without the extra combo box.
        
        schrodinger.application.matsci.reordergui.ReorderAtomsDialog: A Window-Modal dialog that allows the user to reorder atoms in a comparison structure based on a reference structure.
        
        schrodinger.application.desmond.cwidget.StartDialogBase
        
        schrodinger.application.desmond.cwidget.StartDialog1
        
        schrodinger.application.desmond.cwidget.StartDialog2
        
        schrodinger.application.bioluminate.propfilter.ValueSelectionDialog: A SFilteredListWidget that allows the user to select certain values of a property for the criterion.
        
        schrodinger.application.desmond.gui._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
        
        schrodinger.application.desmond.gui.MdcAdvancedDialog: Advanced Options dialog for Mdc Desmond panels
        
        schrodinger.application.desmond.gui.MinAdvancedDialog: Advanced Minimization options dialog for Desmond panels
      - PyQt4.QtGui.QDockWidget: QDockWidget(QString, QWidget parent=None, Qt.WindowFlags flags=0) QDockWidget(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget: The dock widget that can set a ViewerWindow as the main widget.
      - PyQt4.QtGui.QFrame: QFrame(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.desmond.gui_v2.HorizontalBar
        
        schrodinger.application.desmond.gui.HorizontalBar
        
        schrodinger.application.desmond.fep_gui.HorizontalBar
        
        PyQt4.QtGui.QAbstractScrollArea: QAbstractScrollArea(QWidget parent=None)
        
        PyQt4.QtGui.QAbstractItemView: QAbstractItemView(QWidget parent=None)
        
        PyQt4.QtGui.QListView: QListView(QWidget parent=None)
        
        PyQt4.QtGui.QListWidget: QListWidget(QWidget parent=None)
        
        schrodinger.ui.qt.swidgets.SListWidget: A QListWidget that can set its items and set up a callback at creation.
        
        schrodinger.ui.qt.swidgets.SFilteredListWidget: An SListWidget with an additional line edit that can be used to filter the items within the ListWidget
        
        schrodinger.application.bioluminate.propfilter.SelectingFilteredListWidget: A QListWidget that contains a edit to allow the user to filter the contents of the widget.
        
        schrodinger.application.matsci.reordergui.StructureListWidget: A QListWidget that interacts with a structure picture to select atoms.
        
        schrodinger.application.matsci.reordergui.ComparisonListWidget: The list widget for the Comparison structure.
        
        schrodinger.application.matsci.reordergui.ReferenceListWidget: The ListWidget for the reference structure.
        
        PyQt4.QtGui.QTableView: QTableView(QWidget parent=None)
        
        PyQt4.QtGui.QTableWidget: QTableWidget(QWidget parent=None) QTableWidget(int, int, QWidget parent=None)
        
        schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable: Table that is used to show and carry out actions on all databases loaded by user.
        
        schrodinger.application.jaguar.gui.utils.PropertiesTableWidget: A QTableWidget for the Properties table on the Properties tab
        
        schrodinger.application.jaguar.gui.input_tab_widgets.SelectedEntriesView: The view for the selected entries table
        
        schrodinger.application.jaguar.gui.input_tab_widgets_pka.SelectedEntriesViewPka: The view for the pKa selected entries table
        
        schrodinger.application.bioluminate.antibody.search_results_table.TableView: A table view for both full and split search results.
        
        schrodinger.ui.qt.structtable.ViewerTable
        
        schrodinger.application.combiglide.combenumdock.editableViewerTable
        
        PyQt4.QtGui.QGraphicsView: QGraphicsView(QWidget parent=None) QGraphicsView(QGraphicsScene, QWidget parent=None)
        
        schrodinger.application.combiglide.combenumdock._StructView
        
        schrodinger.ui.sketcher.sketcherView
        
        schrodinger.ui.qt.structure2d.structure_view: View which holds a structure_item object
        
        schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView: This class is a subclass of a QGraphicsView that holds a single structure_item, to display a single 2D structure.
        
        schrodinger.application.matsci.reordergui.StructureView: View which holds a structure_item object
        
        PyQt4.QtGui.QLabel: QLabel(QWidget parent=None, Qt.WindowFlags flags=0) QLabel(QString, QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.desmond.cwidget.AdvLabel: A mutli-line label with small, bold text.
        
        schrodinger.application.desmond.fep_gui.AdvLabel: A mutli-line label with small, bold text.
        
        schrodinger.application.bioluminate.pml_menus.ColorLabel: A label that shows off the color each element will be colored if this menu item is chosen.
        
        PyQt4.QtGui.QSplitter: QSplitter(QWidget parent=None) QSplitter(Qt.Orientation, QWidget parent=None)
        
        schrodinger.ui.sequencealignment.sequence_viewer.SequenceViewer: The sequence viewer widget displays and manipulates sequences and associated data.
        
        schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer: Creates a sequence viewer that can be opened by an action or added to a main window as a dockable item.
        
        schrodinger.application.matsci.qualityslider.QualitySlider: A widget that allows the user to see and edit the Jaguar keywords for three different accuracy levels.
        
        schrodinger.application.matsci.reordergui.ReorderAtomFrame: A frame which allows the user to reorder the atoms of a comparison structure based on the atom order of a reference structure.
        
        schrodinger.application.bioluminate.protein_report_widget.ReportFrame: A QtGui.QFrame that contains a Protein Report
        
        schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart: A Protein Report widget that can deal with multiple protein structures and also has a slider chart that can be used to select residues.
        
        schrodinger.application.bioluminate.pml_menus.ResultsWindow
        
        schrodinger.application.bioluminate.sliderchart.SliderPlot: A chart that contains four lines the user can slide to select a region of the chart.
        
        schrodinger.application.matsci.reordergui.StructureFrame: A QFrame that contains a 2D image of a structure.
        
        schrodinger.application.matsci.reordergui.ComparisonFrame: The StructureFrame for the Comparison structure
        
        schrodinger.application.matsci.reordergui.ReferenceFrame: The StructureFrame for the Reference structure
      - PyQt4.QtGui.QGroupBox: QGroupBox(QWidget parent=None) QGroupBox(QString, QWidget parent=None)
        
        schrodinger.application.desmond.gui.AtomGroupFrame: Frame for the "Atom group" box of the Misc tab of the Advanced Options dialog.
        
        schrodinger.application.desmond.gui.InputGroup: Group Frame for showing the widgets for loading the system model.
        
        schrodinger.application.desmond.gui.MinOutputFrame: Group box "Output" of the "Minimization" tab of Advanced Options dialog.
        
        schrodinger.application.desmond.gui.MinimizerFrame: Group box "Minimizer" of the "Minimization" tab of Advanced Options dialog.
        
        schrodinger.application.desmond.gui.RandVelFrame: Frame for the "Randomize velocities" group of the Misc tab of Advanced dialog.
        
        schrodinger.application.desmond.gui._BaseGroup: Enherited by MdGroup and MinimizeGroup, so therefore by all Simulation frames
        
        schrodinger.application.desmond.gui.MdGroup: Molecular Dynamics group
        
        schrodinger.application.desmond.fep_gui._ProtItem: Frame for each checkable group of the second tab of the panel (Plan Calculation).
        
        schrodinger.application.desmond.cwidget._SdIncorpFrame: The incorporation (output) frame of the start dialog.
        
        schrodinger.application.desmond.cwidget._SdJobFrame: Frame for the master job options
        
        schrodinger.application.desmond.cwidget._SdMasterjob
        
        schrodinger.application.desmond.cwidget._SdSubjobFrame
      - PyQt4.QtGui.QLineEdit: QLineEdit(QWidget parent=None) QLineEdit(QString, QWidget parent=None)
        
        schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit: A line edit that can be used to select a basis set.
        
        schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetEditor: A version of the BasisSelectorLineEdit that automatically sets the vertical placement of the pop up based on the constraints of the table size.
        
        schrodinger.application.bioluminate.bwidgets.NumericLineEdit: A QtGui.QLineEdit with a builtin validator for floats or integers.
        
        schrodinger.ui.qt.swidgets.SLineEdit: A QLineEdit that accepts a validator as one of its arguments
        
        schrodinger.application.matsci.atomicsymbolsgui.ElementEdit: A QLineEdit that only accepts atomic symbols and always contains the last valid value when it loses keyboard focus
        
        schrodinger.ui.qt.swidgets.SLabeledEdit: An SLineEdit that has a label attached to it.
        
        schrodinger.application.matsci.qualityslider.KeywordEdit: A swidgets.SLabeledEdit for displaying, editing and retrieving Jaguar keywords.
      - PyQt4.QtGui.QMainWindow: QMainWindow(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.ui.qt.appframework.AppFramework: The AppFramework class is basically a hull for applications.
        
        schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog: A class which displays a dialog with a plot of the statistics for the most recent clustering
        
        schrodinger.application.canvas.clustergui.DendrogramPlotDialog: A class which displays a dialog with a plot of the dendrogram from the most recent clustering
        
        schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog: A class which displays a dialog with a plot of the distance matrix associated with the most recent clustering
        
        schrodinger.application.desmond.gui_v2.GuiApp: Base class of several Desmond panel GUI's (see its subclasses below).
        
        schrodinger.application.desmond.gui.GuiApp: Base class of several Desmond panel GUI's (see its subclasses below).
        
        schrodinger.application.moldescriptors.gui.MainUI: Launching the appframework for the GUI.
        
        schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer: The Main Panel Class
        
        schrodinger.ui.chooseligand.TestApp: Class for testing this module.
        
        schrodinger.application.desmond.fep_gui._App: Class shared by Desmond and Mcpro applications
        
        schrodinger.application.desmond.fep_gui.DesmondApp: Class shared by all Desmond panels.
        
        schrodinger.application.desmond.fep_gui.McproApp: Class shared by all Mcpro panels
        
        schrodinger.application.jaguar.gui.edit_dialog.EditDialog: A dialog that allows JaguarInput objects to be directly edited.
        
        schrodinger.application.bioluminate.ssv.viewer.ViewerWindow: Provides the SimplifiedSequenceViewer with a window to occupy.
        
        schrodinger.ui.sketcher.sketcher
      - PyQt4.QtGui.QMenu: QMenu(QWidget parent=None) QMenu(QString, QWidget parent=None)
        
        schrodinger.application.bioluminate.pml_menus.ColorByElementSubMenu: The Color by Element submenu
        
        schrodinger.application.bioluminate.pml_menus.PMLMenu: The base menu class we subclass from
        
        schrodinger.application.bioluminate.pml_menus.ActionMenu: The Action menu
        
        schrodinger.application.bioluminate.pml_menus.AroundExpandSubMenu: The modify-around submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.AsMenu: The Show->As submenu
        
        schrodinger.application.bioluminate.pml_menus.AutoColorSubMenu: The Color menu
        
        schrodinger.application.bioluminate.pml_menus.ColorChainSubMenu: The ColorChainSubMenu menu
        
        schrodinger.application.bioluminate.pml_menus.ColorMenu: The Color menu
        
        schrodinger.application.bioluminate.pml_menus.ColorSpectrumSubMenu: The ColorSpectrumSubMenu menu
        
        schrodinger.application.bioluminate.pml_menus.ColorSubstructureSubMenu: The ColorSubstructureSubMenu menu
        
        schrodinger.application.bioluminate.pml_menus.CompleteSubMenu: The modify-complete submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.ComputeSubMenu: The Action Compute submenu
        
        schrodinger.application.bioluminate.pml_menus.EntrySubMenu: A submenu that lists all enabled Entry objects
        
        schrodinger.application.bioluminate.pml_menus.ExcludeSubMenu: The modify-exclude submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.ExtendSubMenu: The modify-extend submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.FindPCSubMenu: The Find Polar Contacts submenu
        
        schrodinger.application.bioluminate.pml_menus.GenSelectionSubMenu: The Action Generate Selection submenu
        
        schrodinger.application.bioluminate.pml_menus.GenSymMatesSubMenu: The Action Generate Symmetry Mates submenu
        
        schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu: The submenu that contains all the main actions used for most context menus
        
        schrodinger.application.bioluminate.pml_menus.ObjectFreeContextSubMenu: The GeneralContextSubMenu for a right-click that is not on an object
        
        schrodinger.application.bioluminate.pml_menus.SubstructureContextSubMenu: The GeneralContextSubMenu for a right-click that is on an atom
        
        schrodinger.application.bioluminate.pml_menus.GenerateSubMenu: The Action Generate submenu
        
        schrodinger.application.bioluminate.pml_menus.HideHydrogenSubMenu: The Hide Hydrogen submenu
        
        schrodinger.application.bioluminate.pml_menus.HideMenu: The Hide menu
        
        schrodinger.application.bioluminate.pml_menus.HydrogenSubMenu: The Action Hydrogen submenu
        
        schrodinger.application.bioluminate.pml_menus.IncludeSubMenu: The modify-include submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.InvertSubMenu: The modify-invert submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomIdentSubMenu: The Label Atom Identifiers submenu
        
        schrodinger.application.bioluminate.pml_menus.LabelMenu: The Label menu
        
        schrodinger.application.bioluminate.pml_menus.LabelOtherSubMenu: The Label Other Properties submenu
        
        schrodinger.application.bioluminate.pml_menus.LigandSitesSubMenu: The Action-Preset-Ligand Sites submenu
        
        schrodinger.application.bioluminate.pml_menus.ModifySubMenu: The modify submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.PMLContextMenu: The base menu class we subclass from for context menus
        
        schrodinger.application.bioluminate.pml_menus.AtomContextMenu: The context menu for right-clicks on non-selected atoms
        
        schrodinger.application.bioluminate.pml_menus.SelectedAtomContextMenu: The context menu for right-clicks on selected atoms
        
        schrodinger.application.bioluminate.pml_menus.SpaceContextMenu: The context menu for right-clicks in space
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsSubMenu: The Polar Contacts submenu
        
        schrodinger.application.bioluminate.pml_menus.PresetSubMenu: The Preset submenu
        
        schrodinger.application.bioluminate.pml_menus.RestrictSubMenu: The modify-restrict submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.SelectedAtomContextActionSubMenu: The submenu that allows the user to enable/disable individual objects
        
        schrodinger.application.bioluminate.pml_menus.SelectionSubMenu: A submenu that lists all enabled Entry objects
        
        schrodinger.application.bioluminate.pml_menus.ShowMenu: The Show menu
        
        schrodinger.application.bioluminate.pml_menus.SurfaceAreaSubMenu: The Action Surface Area submenu
        
        schrodinger.application.bioluminate.pml_menus.ToggleStateSubMenu: The submenu that allows the user to enable/disable individual objects
        
        schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu: A submenu that shows the most recently chosen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.RecentCarbonColorSubMenu: A submenu that shows the most recently chosen carbon colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.RecentHydrogenColorSubMenu: A submenu that shows the most recently chosen hydrogen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.RecentObjectColorSubMenu: A submenu that shows the most recently chosen object colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.ShowOrganicMenu: The Show->Organic submenus
        
        schrodinger.application.bioluminate.pml_menus.ShowSubstructureMenu: The Show->substructure submenus
      - PyQt4.QtGui.QToolBar: QToolBar(QString, QWidget parent=None) QToolBar(QWidget parent=None)
        
        schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar: Get the toolbar that has the combobox with the antibody numering schemes.
        
        schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar: A toolbar associated with the viewer that will handle display options.
        
        schrodinger.application.bioluminate.ssv.toolbars.FindToolBar: Create an instance of the "Find Pattern" toolbar from the MSV.
        
        schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar: Get the toolbar that has the import dialogs.
        
        schrodinger.ui.sketcher.sketcherGUIMultiColumnToolBar
      - schrodinger.application.moldescriptors.gui.QikPropUI
      - schrodinger.application.desmond.gui.RelaxFrame: Frame that includes the "Relax model..." check box and the relaxation protocol entry field.
      - schrodinger.application.desmond.gui.RestraintsTab: Frame for the Restraints tab of the Advanced Options dialog
      - schrodinger.application.bioluminate.bwidgets.RowActionItem: Custom widget to be used in a table cell.
      - schrodinger.application.desmond.gui.SimOptionsFrame: Responsible for drawing the simulation options widgets, including Simulation time and Recording intervals.
      - schrodinger.application.jaguar.gui.theory_tab_widgets.SpinRestrictedWidget: This widget allows user to specify SCF spin treatment options.
      - schrodinger.application.bioluminate.antibody.search_results_table.SplitTable: A widget to contain both split search results tables (i.e.
      - schrodinger.application.desmond.fep_gui._DesmondProt: Frame for the second tab ("Plan Calculation") of the Desmond GUIs.
      - schrodinger.application.desmond.fep_gui._McproProt: Frame for the second tab ("Plan Calculation") of the Mcpro GUIs.
      - schrodinger.application.desmond.fep_gui._Pert: Frame for the bottom part of the "Plan Calculation" tab of Mcpro GUIs.
      - schrodinger.application.desmond.cwidget._SdDetailFrame: Frame for the section that gets shown when the "Detail" button is toggled on.
  - PyQt4.QtGui.QWidget.RenderFlags: QWidget.RenderFlags(QWidget.RenderFlags) QWidget.RenderFlags(int) QWidget.RenderFlags()
  - PyQt4.QtGui.QGraphicsScene.SceneLayers: QGraphicsScene.SceneLayers(QGraphicsScene.SceneLayers) QGraphicsScene.SceneLayers(int) QGraphicsScene.SceneLayers()
  - PyQt4.QtGui.QAbstractSpinBox.StepEnabled: QAbstractSpinBox.StepEnabled(QAbstractSpinBox.StepEnabled) QAbstractSpinBox.StepEnabled(int) QAbstractSpinBox.StepEnabled()
  - sip.wrapper
    - schrodinger.infra._canvas2d.ChemViewAnnotator
    - PyQt4.QtGui.QGraphicsItem: QGraphicsItem(QGraphicsItem parent=None, QGraphicsScene scene=None)
      - schrodinger.application.combiglide.combenumdock._StructViewItem
      - schrodinger.application.combiglide.combenumdock._zoomViewItem
      - schrodinger.ui.sketcher.sketcherGraphicalObject
        
        schrodinger.ui.sketcher.sketcherAtom
        
        schrodinger.ui.sketcher.sketcherResidue
        
        schrodinger.ui.sketcher.sketcherBond
        
        schrodinger.ui.sketcher.sketcherResidueInteraction
      - schrodinger.ui.qt.structure2d.structure_item
        
        schrodinger.application.matsci.reordergui.StructurePic: The QGraphicsItem that holds a 2D image of a structure
    - PyQt4.QtCore.QObject: QObject(QObject parent=None)
      - schrodinger.application.desmond.gui_v2.AdvOptionsFrame: Frame for the "Advanced Options" button.
      - schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab: Base class for all properties tab subtabs.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab: This sub tab class is used for ESP property.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.MullikenSubTab: This sub tab class is used for Mulliken property.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab: This sub tab class is used for Multipole property.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab: This sub tab class is used for Polarizability property.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.RamanSubTab
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab: This sub tab class is used for Surfaces property.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab: This sub tab class is used for Vibrational property.
      - schrodinger.application.combiglide.connection_storage.ConnectionStorage: This class is used to store the data of the current connection table.
        
        schrodinger.application.combiglide.combenumdock.ConnectionStorage: This class is used to store the data of the current connection table.
      - schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker: This class is responsible for atom and bond picking.
      - PyQt4.QtGui.QAbstractItemDelegate: QAbstractItemDelegate(QObject parent=None)
        
        PyQt4.QtGui.QItemDelegate: QItemDelegate(QObject parent=None)
        
        schrodinger.application.desmond.gui_v2.AtomGroupDelegate: Class for allowing the data in the AtomGroupModel to be modified.
        
        schrodinger.application.desmond.gui.AtomGroupDelegate: Class for allowing the data in the AtomGroupModel to be modified.
        
        schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate: This delegate is used to validate values entered in 'target value' column.
        
        schrodinger.application.desmond.gui.PosResDelegate: Class for allowing the data in the PosResModel to be modified
        
        schrodinger.application.desmond.gui_v2.PosResDelegate: Class for allowing the data in the PosResModel to be modified
        
        schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate: This delegate is used to define how float coordinate values are displayed in a line edit widget.
        
        schrodinger.application.desmond.gui.TempItemDelegate: Class for allowing the data in the TableModel to be modified.
        
        schrodinger.application.desmond.gui_v2.TempItemDelegate: Class for allowing the data in the TableModel to be modified.
        
        schrodinger.ui.qt.structtable._GenericViewerDelegate: This is the class that handles the actual drawing of data.
        
        schrodinger.ui.qt.structtable.StructureViewerDelegate
        
        schrodinger.ui.qt.structtable.StructureReaderDelegate
        
        schrodinger.application.combiglide.combenumdock.createFragmentDelegate
        
        schrodinger.application.combiglide.combenumdock.simpleEnumDockDelegate
        
        PyQt4.QtGui.QStyledItemDelegate: QStyledItemDelegate(QObject parent=None)
        
        schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetDelegate: A delegate for selecting a basis set.
        
        schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate: A delegate where Ctrl+Enter will cause the value to be committed to all selected rows.
        
        schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate: A delegate for selecting a pKa atom.
        
        schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate: A spin box delegate.
        
        schrodinger.application.jaguar.gui.input_tab_widgets.WorkspaceInclusionDelegate: A delegate for representing workspace inclusion as it is shown in the project table.
      - PyQt4.QtCore.QAbstractItemModel: QAbstractItemModel(QObject parent=None)
        
        PyQt4.QtCore.QAbstractListModel: QAbstractListModel(QObject parent=None)
        
        schrodinger.ui.ligfilter.CriteriaListModel: Class for storing the criteria list information.
        
        schrodinger.application.bioluminate.propfilter.CriteriaListModel: Class for storing the criteria list information.
        
        PyQt4.QtGui.QAbstractProxyModel: QAbstractProxyModel(QObject parent=None)
        
        PyQt4.QtGui.QSortFilterProxyModel: QSortFilterProxyModel(QObject parent=None)
        
        schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesProxyModel: A proxy model that allows to hide columns.
        
        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.
        
        schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel: A proxy model that allows to hide columns.
        
        schrodinger.application.jaguar.gui.input_tab_widgets.SelectedEntriesProxyModel: The proxy model for the selected entries table
        
        PyQt4.QtCore.QAbstractTableModel: QAbstractTableModel(QObject parent=None)
        
        schrodinger.application.desmond.gui.AtomGroupModel: Class for storing the window table information.
        
        schrodinger.application.desmond.gui_v2.AtomGroupModel: Class for storing the window table information.
        
        schrodinger.ui.chooseligand.ChooseLigandModel
        
        schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel: A base class for cordinates models used for constraint and scan coordinates in Scan and Optimization tabs.
        
        schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel: A model to store scan tab coordinates data.
        
        schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel: A model to store scan tab coordinates data.
        
        schrodinger.application.bioluminate.protein_report_widget.DataModel: Class for storing the table information.
        
        schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart: A subclass of DataModel that calls a sort callback when sorting
        
        schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel: A model to store search results
        
        schrodinger.application.desmond.fep_gui.PathModel: Class for storing table information.
        
        schrodinger.ui.ligfilter.PatternModel: Class for strring patterns (definitions) and their groups
        
        schrodinger.application.desmond.gui.PosResModel: Class for storing the window table information.
        
        schrodinger.application.desmond.gui_v2.PosResModel: Class for storing the window table information.
        
        schrodinger.application.desmond.fep_gui.ResiduesModel: Class for storing the residues table information.
        
        schrodinger.application.jaguar.gui.input_tab_widgets.SelectedEntriesModel: The data model for the selected entries table
        
        schrodinger.application.jaguar.gui.input_tab_widgets_hb.SelectedEntriesModelHB: The data model for the HB selected entries table.
        
        schrodinger.application.jaguar.gui.input_tab_widgets_pka.SelectedEntriesModelPka: The data model for the pKa selected entries table
        
        schrodinger.application.desmond.fep_gui.StrucListModel: Class for storing table information.
        
        schrodinger.application.desmond.gui_v2.TableModel: Class for storing the window table information.
        
        schrodinger.application.desmond.gui.TableModel: Class for storing the window table information.
        
        schrodinger.ui.qt.table.ViewerModel
        
        schrodinger.ui.qt.structtable.ViewerModel: This class has been moved to the new table module
        
        schrodinger.application.combiglide.combenumdock.collectionViewerModel
      - PyQt4.QtGui.QAction: QAction(QObject) QAction(QString, QObject) QAction(QIcon, QString, QObject)
        
        schrodinger.application.bioluminate.pml_menus.MAction: A QAction that performs a Maestro command
        
        schrodinger.application.bioluminate.pml_menus.AddHydrogens
        
        schrodinger.application.bioluminate.pml_menus.AutoColorObjects
        
        schrodinger.application.bioluminate.pml_menus.AutoColorCarbons
        
        schrodinger.application.bioluminate.pml_menus.AutoCycleColor
        
        schrodinger.application.bioluminate.pml_menus.AutoCycleCarbonColor
        
        schrodinger.application.bioluminate.pml_menus.Center
        
        schrodinger.application.bioluminate.pml_menus.Clean
        
        schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor
        
        schrodinger.application.bioluminate.pml_menus.ColorCalphasByBFactor
        
        schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum
        
        schrodinger.application.bioluminate.pml_menus.ColorCalphasBySpectrum
        
        schrodinger.application.bioluminate.pml_menus.ColorCarbonsBySpectrum
        
        schrodinger.application.bioluminate.pml_menus.ColorChainbows
        
        schrodinger.application.bioluminate.pml_menus.ColorChains
        
        schrodinger.application.bioluminate.pml_menus.ColorChainsByCalpha
        
        schrodinger.application.bioluminate.pml_menus.ColorChainsByCarbon
        
        schrodinger.application.bioluminate.pml_menus.ColorHNOS
        
        schrodinger.application.bioluminate.pml_menus.ComputeSurfaceArea
        
        schrodinger.application.bioluminate.pml_menus.CountAtoms
        
        schrodinger.application.bioluminate.pml_menus.CreateEntry
        
        schrodinger.application.bioluminate.pml_menus.CustomColor
        
        schrodinger.application.bioluminate.pml_menus.ColorCarbons
        
        schrodinger.application.bioluminate.pml_menus.ColorHydrogens
        
        schrodinger.application.bioluminate.pml_menus.ColorObject
        
        schrodinger.application.bioluminate.pml_menus.DeleteAll
        
        schrodinger.application.bioluminate.pml_menus.DeleteAtoms
        
        schrodinger.application.bioluminate.pml_menus.DeleteProject
        
        schrodinger.application.bioluminate.pml_menus.DeleteSelections
        
        schrodinger.application.bioluminate.pml_menus.DeleteWS
        
        schrodinger.application.bioluminate.pml_menus.Disable
        
        schrodinger.application.bioluminate.pml_menus.Duplicate
        
        schrodinger.application.bioluminate.pml_menus.ExcludeInorganicFromSelection
        
        schrodinger.application.bioluminate.pml_menus.ExcludeOrganicFromSelection
        
        schrodinger.application.bioluminate.pml_menus.ExcludePolymerFromSelection
        
        schrodinger.application.bioluminate.pml_menus.ExcludeSolventFromSelection
        
        schrodinger.application.bioluminate.pml_menus.ExcludeVisibleFromSelection
        
        schrodinger.application.bioluminate.pml_menus.Expand: Expand the selection to the atoms around the ASL for this object
        
        schrodinger.application.bioluminate.pml_menus.Around
        
        schrodinger.application.bioluminate.pml_menus.Extend: Expand the selection to the atoms within X bonds of the ASL for this object
        
        schrodinger.application.bioluminate.pml_menus.GenerateSelection: Select the atoms, then generate a selection object from them
        
        schrodinger.application.bioluminate.pml_menus.GenerateInterfaceSelection
        
        schrodinger.application.bioluminate.pml_menus.GenerateLigandSelection
        
        schrodinger.application.bioluminate.pml_menus.GenerateSurfResSelection
        
        schrodinger.application.bioluminate.pml_menus.GenerateSymmetryMates: Generate all the symmetry mates and show those within X angstroms
        
        schrodinger.application.bioluminate.pml_menus.HideAllOthers
        
        schrodinger.application.bioluminate.pml_menus.HideAtoms
        
        schrodinger.application.bioluminate.pml_menus.HideEverything
        
        schrodinger.application.bioluminate.pml_menus.HideHydrogens
        
        schrodinger.application.bioluminate.pml_menus.HideLabel
        
        schrodinger.application.bioluminate.pml_menus.HideMainChain
        
        schrodinger.application.bioluminate.pml_menus.HideNonBonded
        
        schrodinger.application.bioluminate.pml_menus.HidePolarHydrogens
        
        schrodinger.application.bioluminate.pml_menus.HideRibbons
        
        schrodinger.application.bioluminate.pml_menus.HideSideChain
        
        schrodinger.application.bioluminate.pml_menus.HideSurface
        
        schrodinger.application.bioluminate.pml_menus.HideSymmetryMates
        
        schrodinger.application.bioluminate.pml_menus.HideWaters
        
        schrodinger.application.bioluminate.pml_menus.IncludeVisibleInSelection
        
        schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection: Invert or complete the selection within an object
        
        schrodinger.application.bioluminate.pml_menus.SelectWithinAny
        
        schrodinger.application.bioluminate.pml_menus.SelectWithinCalpha
        
        schrodinger.application.bioluminate.pml_menus.SelectWithinChain
        
        schrodinger.application.bioluminate.pml_menus.SelectWithinEntry
        
        schrodinger.application.bioluminate.pml_menus.SelectWithinMolecule
        
        schrodinger.application.bioluminate.pml_menus.SelectWithinResidue
        
        schrodinger.application.bioluminate.pml_menus.LabelAtom: A QAction that performs labels atoms with the given label
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomByProp: Labels all atoms by a custom atom property
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomByEntryIndex
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomByMolIndex
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomByNumType
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomByOccupancy
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomByVDW
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomByStereo
        
        schrodinger.application.bioluminate.pml_menus.LabelChains
        
        schrodinger.application.bioluminate.pml_menus.LabelResidues
        
        schrodinger.application.bioluminate.pml_menus.MakeProjectEntry: Copies the atoms into a new project entry and includes it in the workspace
        
        schrodinger.application.bioluminate.pml_menus.Orient
        
        schrodinger.application.bioluminate.pml_menus.Origin
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsObject
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsOnlyMainchain
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsOnlySidechain
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyAtoms
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyNonSolvent
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsToEntry
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsToEntryWithoutSolvent
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsWithSidechains
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsWithSolvent
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutIntraMainchain
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutMainchain
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutSolvent
        
        schrodinger.application.bioluminate.pml_menus.PresetAction: Base class for Preset Actions
        
        schrodinger.application.bioluminate.pml_menus.AntibodyPreset
        
        schrodinger.application.bioluminate.pml_menus.BAndSPreset
        
        schrodinger.application.bioluminate.pml_menus.BFactorPreset
        
        schrodinger.application.bioluminate.pml_menus.DefaultPreset
        
        schrodinger.application.bioluminate.pml_menus.InterfacePreset
        
        schrodinger.application.bioluminate.pml_menus.LigandPreset
        
        schrodinger.application.bioluminate.pml_menus.PrettyPubPreset: Show the object as nice-looking cartoon ribbons
        
        schrodinger.application.bioluminate.pml_menus.SimplePreset
        
        schrodinger.application.bioluminate.pml_menus.TechnicalPreset
        
        schrodinger.application.bioluminate.pml_menus.Quit
        
        schrodinger.application.bioluminate.pml_menus.Ray: Use PyMOL to make a ray-traced image
        
        schrodinger.application.bioluminate.pml_menus.Reinitialize
        
        schrodinger.application.bioluminate.pml_menus.RemoveHydrogens
        
        schrodinger.application.bioluminate.pml_menus.RemovePC
        
        schrodinger.application.bioluminate.pml_menus.RemoveWaters
        
        schrodinger.application.bioluminate.pml_menus.Rename
        
        schrodinger.application.bioluminate.pml_menus.RestrictSelection: Restrict the selection to a specific object
        
        schrodinger.application.bioluminate.pml_menus.ExcludeFromSelection
        
        schrodinger.application.bioluminate.pml_menus.IncludeInSelection: Include a specific object in the selection
        
        schrodinger.application.bioluminate.pml_menus.RestrictToInorganic
        
        schrodinger.application.bioluminate.pml_menus.RestrictToOrganic
        
        schrodinger.application.bioluminate.pml_menus.RestrictToPolymer
        
        schrodinger.application.bioluminate.pml_menus.RestrictToSolvent
        
        schrodinger.application.bioluminate.pml_menus.RestrictToVisible
        
        schrodinger.application.bioluminate.pml_menus.Select
        
        schrodinger.application.bioluminate.pml_menus.ShowBAndS
        
        schrodinger.application.bioluminate.pml_menus.ShowCartoonOrRibbon
        
        schrodinger.application.bioluminate.pml_menus.ShowCartoon
        
        schrodinger.application.bioluminate.pml_menus.ShowRibbon
        
        schrodinger.application.bioluminate.pml_menus.ShowLabel
        
        schrodinger.application.bioluminate.pml_menus.ShowLines
        
        schrodinger.application.bioluminate.pml_menus.ShowLigandLines
        
        schrodinger.application.bioluminate.pml_menus.ShowNonBonded
        
        schrodinger.application.bioluminate.pml_menus.ShowNonBondedSpheres
        
        schrodinger.application.bioluminate.pml_menus.ShowSpheres
        
        schrodinger.application.bioluminate.pml_menus.ShowLigandSpheres
        
        schrodinger.application.bioluminate.pml_menus.ShowTubes
        
        schrodinger.application.bioluminate.pml_menus.ShowLigandTubes
        
        schrodinger.application.bioluminate.pml_menus.SumFormalCharge
        
        schrodinger.application.bioluminate.pml_menus.SumPartialCharge
        
        schrodinger.application.bioluminate.pml_menus.SurfaceRender: Base class for actions that render a surface
        
        schrodinger.application.bioluminate.pml_menus.ShowMesh
        
        schrodinger.application.bioluminate.pml_menus.ShowSurface
        
        schrodinger.application.bioluminate.pml_menus.ToggleState: A MAction that toggles the enabled/disabled state of an object
        
        schrodinger.application.bioluminate.pml_menus.Zoom
        
        PyQt4.QtGui.QWidgetAction: QWidgetAction(QObject)
        
        schrodinger.application.bioluminate.pml_menus.MWidgetAction: A QAction that performs a Maestro command
        
        schrodinger.application.bioluminate.pml_menus.ColorBySubstructure
        
        unreachable.CustomRecentColor
        
        schrodinger.application.bioluminate.pml_menus.ColorRecentCarbons
        
        schrodinger.application.bioluminate.pml_menus.ColorRecentHydrogens
        
        schrodinger.application.bioluminate.pml_menus.ColorRecentObjects
        
        schrodinger.application.bioluminate.pml_menus.CustomRecentColor
        
        schrodinger.application.bioluminate.actions.factory.SAction: A QAction that enforces standards that are expected by some BioLuminate methods.
      - PyQt4.QtGui.QGraphicsScene: QGraphicsScene(QObject parent=None) QGraphicsScene(QRectF, QObject parent=None) QGraphicsScene(float, float, float, float, QObject parent=None)
        
        schrodinger.ui.sketcher.sketcherScene
      - PyQt4.QtGui.QMovie: QMovie(QObject parent=None) QMovie(QIODevice, QByteArray format=QByteArray(), QObject parent=None) QMovie(QString, QByteArray format=QByteArray(), QObject parent=None)
        
        schrodinger.application.bioluminate.bwidgets.LoadingIcon: Animates a "loading" icon that can be used by any Qt object that has the C{setIcon} method.
      - PyQt4.QtGui.QValidator: QValidator(QObject parent=None)
        
        schrodinger.application.matsci.atomicsymbolsgui.ElementValidator: A QValidator to check if the input is a partial or valid atomic symbol.
        
        PyQt4.QtGui.QIntValidator: QIntValidator(QObject parent=None) QIntValidator(int, int, QObject parent=None)
        
        schrodinger.application.desmond.cwidget.CpuValidator
        
        schrodinger.application.jaguar.gui.basis_selector.UpperCaseValidator: A QValidator that converts all input to uppercase
      - PyQt4.QtGui.QWidget: QWidget(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.desmond.gui.AdvOptionsFrame: Frame for the "Advanced Options" button.
        
        schrodinger.ui.qt.appframework2.baseapp.BasePanel
        
        schrodinger.ui.qt.appframework2.baseapp.ValidatedPanel
        
        schrodinger.ui.qt.appframework2.af2.App
        
        schrodinger.ui.qt.appframework2.af2.JobApp
        
        schrodinger.application.jaguar.gui.base_panel.BasePanel: A base class for all Jaguar GUIs.
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanel: A convenience class for standard Jaguar panels that:
        
        schrodinger.application.jaguar.gui.base_panel.StandardPanelNoInputTab: A convenience class for standard Jaguar panels that use a "Molecule" tab (with a basis selector) in place of an "Input" tab.
        
        schrodinger.application.jaguar.gui.base_panel.MultiStructurePanel: A convenience class for standard Jaguar panels that use a MultiStructureTab.
        
        schrodinger.application.matsci.reordergui.ReorderAtomPanel: A simple panel that takes two selected entries and allows one of them to be reordered - this is mainly for testing and example purposes.
        
        schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab: The base class for all Jaguar tabs.
        
        schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab: A parent class for the Scan and Optimization tabs
        
        schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab
        
        schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase: A tab for specifying settings for the structures currently selected in the project table.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTab: An input tab that allows the user to specify basis sets.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB: An input tab that is used with Hydrogen Bond task.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka: An input tab that allows the user to specify pKa atoms.
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase: The base class for all molecule tabs.
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab: The standard molecule tab
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector: A Molecule tab that does not use the input selector
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka: The molecule tab used in the PKA panel
        
        schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab: A parent class for tabs that allow transition state, reactant, and product structures to be selected.
        
        schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab
        
        schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab
        
        schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab: Output tab for the Jaguar panels.
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab
        
        schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabIGO
        
        schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab: " The Molecules tab used in the Reactions panel.
        
        schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab
        
        schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab
        
        schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab: This is the basic SCF tab that is used for majority of tasks.
        
        schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals: This tab is used for SPE and Optimizations tasks and includes the "Use consistent orbital sets when all input structures are isomers" check box
        
        schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabIGO: This tab is used for 'Initial Guess Only' task.
        
        schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab: The Solvent tab using in the pKa panel
        
        schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab: The Solvation tab, which includes solvent model and gas-phase reference energy
        
        schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab: A tab for selecting the level of theory.
        
        schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization: This tab is used for 'Optimization' task.
        
        schrodinger.application.jaguar.gui.basis_selector.BasisSelector: A widget for selecting a Jaguar basis set.
        
        schrodinger.application.jaguar.gui.basis_selector._BasisSelectorPopUp: The pop up window that is displayed adjacent to BasisSelectorLineEdit
        
        schrodinger.application.moldescriptors.gui.DescriptorsUI
        
        schrodinger.application.desmond.gui.EnsembleClassFrame: Frame that includes the Ensemble class pull-down menu and the entry fields correspondint to it.
        
        schrodinger.application.desmond.gui.EnsembleTab: Frame for the Ensemble tab of the Advanced Options dialog.
        
        schrodinger.application.desmond.cwidget.EntryField: A special composite widget which contains a labeled line edit field.
        
        schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget: This widget allows user to specify 'Excited state' options.
        
        schrodinger.application.jaguar.gui.theory_tab_widgets.HFExcitedStateWidget: This widget differs from the parent only by some text, which is specific to HF theory level.
        
        schrodinger.application.desmond.cwidget.FileEntry: Class combining a QLabel, QLineEdit, and a QPushButton (Browse...).
        
        schrodinger.application.bioluminate.antibody.search_results_table.FullTable: A widget to contain the full search results table
        
        schrodinger.application.desmond.fep_gui.HelpLabel: A special composite widget which contains 2 help labels.
        
        schrodinger.application.bioluminate.bwidgets.ImportWidget
        
        schrodinger.application.desmond.gui.IntegrationTab: Frame for the Integration tab of the Mdc Advanced Options dialogs
        
        schrodinger.application.desmond.gui.InteractionTab: Frame for the Interaction frame of the Advanced Options dialog.
        
        schrodinger.ui.ligfilter.LigfilterFrame: Frame for setting up Ligfilter jobs, including property/SMARTS criteria and new definitions.
        
        schrodinger.application.desmond.gui.MdcMiscTab: Frame for the Misc tab of Mdc Advanced Options dialogs.
        
        schrodinger.application.desmond.gui.MinMiscTab: Frame for the Misc Tab of Advanced Options dialog of Minimization GUI.
        
        schrodinger.application.desmond.gui.MinimizationTab: Frame for the Minimization tab of the Advanced Options dialog.
        
        schrodinger.application.moldescriptors.gui.MopacUI
        
        schrodinger.application.desmond.gui.OutputTab: Frame for the Output tab of the Advanced Options dialog
        
        schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin: A mixin for tabs that allow the user to select a basis set.
        
        schrodinger.application.jaguar.gui.tabs.input_tab.InputTab: An input tab that allows the user to specify basis sets.
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab: The standard molecule tab
        
        schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector: A Molecule tab that does not use the input selector
        
        schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab: A parent class for tabs that allow transition state, reactant, and product structures to be selected.
        
        schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab
        
        schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab
        
        PyQt4.QtGui.QAbstractButton: QAbstractButton(QWidget parent=None)
        
        PyQt4.QtGui.QCheckBox: QCheckBox(QWidget parent=None) QCheckBox(QString, QWidget parent=None)
        
        schrodinger.application.desmond.fep_gui.PickAtomToggle: Pick atom widget with a precommand feature.
        
        schrodinger.application.desmond.fep_gui.PickBondToggle: Pick bond widget with a precommand feature.
        
        schrodinger.application.jaguar.gui.utils.WorkspaceInclusionCheckBox: A checkbox that is skinned to look like the Project Table workspace inclusion checkbox.
        
        PyQt4.QtGui.QPushButton: QPushButton(QWidget parent=None) QPushButton(QString, QWidget parent=None) QPushButton(QIcon, QString, QWidget parent=None)
        
        schrodinger.application.bioluminate.bwidgets.QuickHelpButton: A help button that has a blue gradient
        
        PyQt4.QtGui.QAbstractSpinBox: QAbstractSpinBox(QWidget parent=None)
        
        PyQt4.QtGui.QSpinBox: QSpinBox(QWidget parent=None)
        
        schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox: A spin box that allows the empty string as an acceptable value
        
        PyQt4.QtGui.QComboBox: QComboBox(QWidget parent=None)
        
        schrodinger.ui.qt.utils.EnhancedComboBox: A combo box with several Pythonic enhancements
        
        schrodinger.application.jaguar.gui.utils.EnhancedComboBox: A combo box for use in the Jaguar GUI with several Pythonic enhancements
        
        schrodinger.application.desmond.fep_gui.MultiSelectComboBox
        
        PyQt4.QtGui.QDialog: QDialog(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog: Modal dialog window that allows users to set active databases.
        
        schrodinger.ui.ligfilter.AddDefinitionDialog: Frame for generating a pattern definition.
        
        schrodinger.ui.chooseligand.ChooseLigandDialog
        
        schrodinger.application.bioluminate.pml_menus.ColorChooserPanel: A window that lets the user choose a Maestro color.
        
        schrodinger.application.jaguar.gui.base_panel.CoordinateDialog: This dialog allows user to select corrective action when the same coordinate is found in the lists of scans and constraints.
        
        schrodinger.ui.ligfilter.DefinitionViewerDialog: Frame containing a text box with a text display of the definition.
        
        schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog: A dialog for showing exceptions to users
        
        schrodinger.application.bioluminate.propfilter.PropFilterDialog: Panel to allow the user to define criteria for filtering property values
        
        PyQt4.QtGui.QFileDialog: QFileDialog(QWidget, Qt.WindowFlags) QFileDialog(QWidget parent=None, QString caption=QString(), QString directory=QString(), QString filter=QString())
        
        schrodinger.ui.qt.filedialog.FileDialog: File browser dialog with custom sidebar.
        
        schrodinger.application.jaguar.gui.filedialog.FileDialogWithExtraCombo: A Qt file dialog with an extra combo box about the filename text edit
        
        schrodinger.application.jaguar.gui.filedialog.ReadFileDialog: An Open dialog both with an extra combo box to specify whether "Geometry and settings" or "Geometry only" should be read from the specified file.
        
        schrodinger.application.jaguar.gui.filedialog.WriteFileDialog: A Save dialog both with an extra combo box to specify whether an input or a batch file should be written.
        
        schrodinger.application.bioluminate.bwidgets.SequenceFileDialog: Custom class to handle opening files related to sequences.
        
        schrodinger.application.bioluminate.bwidgets.TemplateFileDialog: File dialog specific to templates
        
        schrodinger.application.jaguar.gui.filedialog.WriteFileDialogNoBat: A Save dialog without the extra combo box.
        
        schrodinger.application.matsci.reordergui.ReorderAtomsDialog: A Window-Modal dialog that allows the user to reorder atoms in a comparison structure based on a reference structure.
        
        schrodinger.application.desmond.cwidget.StartDialogBase
        
        schrodinger.application.desmond.cwidget.StartDialog1
        
        schrodinger.application.desmond.cwidget.StartDialog2
        
        schrodinger.application.bioluminate.propfilter.ValueSelectionDialog: A SFilteredListWidget that allows the user to select certain values of a property for the criterion.
        
        schrodinger.application.desmond.gui._BaseAdvancedDialog: Subclass shared by MinAdvancedDialog and MdcAdvancedDialog.
        
        schrodinger.application.desmond.gui.MdcAdvancedDialog: Advanced Options dialog for Mdc Desmond panels
        
        schrodinger.application.desmond.gui.MinAdvancedDialog: Advanced Minimization options dialog for Desmond panels
        
        PyQt4.QtGui.QDockWidget: QDockWidget(QString, QWidget parent=None, Qt.WindowFlags flags=0) QDockWidget(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget: The dock widget that can set a ViewerWindow as the main widget.
        
        PyQt4.QtGui.QFrame: QFrame(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.desmond.gui_v2.HorizontalBar
        
        schrodinger.application.desmond.gui.HorizontalBar
        
        schrodinger.application.desmond.fep_gui.HorizontalBar
        
        PyQt4.QtGui.QAbstractScrollArea: QAbstractScrollArea(QWidget parent=None)
        
        PyQt4.QtGui.QAbstractItemView: QAbstractItemView(QWidget parent=None)
        
        PyQt4.QtGui.QListView: QListView(QWidget parent=None)
        
        PyQt4.QtGui.QListWidget: QListWidget(QWidget parent=None)
        
        schrodinger.ui.qt.swidgets.SListWidget: A QListWidget that can set its items and set up a callback at creation.
        
        schrodinger.ui.qt.swidgets.SFilteredListWidget: An SListWidget with an additional line edit that can be used to filter the items within the ListWidget
        
        schrodinger.application.bioluminate.propfilter.SelectingFilteredListWidget: A QListWidget that contains a edit to allow the user to filter the contents of the widget.
        
        schrodinger.application.matsci.reordergui.StructureListWidget: A QListWidget that interacts with a structure picture to select atoms.
        
        schrodinger.application.matsci.reordergui.ComparisonListWidget: The list widget for the Comparison structure.
        
        schrodinger.application.matsci.reordergui.ReferenceListWidget: The ListWidget for the reference structure.
        
        PyQt4.QtGui.QTableView: QTableView(QWidget parent=None)
        
        PyQt4.QtGui.QTableWidget: QTableWidget(QWidget parent=None) QTableWidget(int, int, QWidget parent=None)
        
        schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable: Table that is used to show and carry out actions on all databases loaded by user.
        
        schrodinger.application.jaguar.gui.utils.PropertiesTableWidget: A QTableWidget for the Properties table on the Properties tab
        
        schrodinger.application.jaguar.gui.input_tab_widgets.SelectedEntriesView: The view for the selected entries table
        
        schrodinger.application.jaguar.gui.input_tab_widgets_pka.SelectedEntriesViewPka: The view for the pKa selected entries table
        
        schrodinger.application.bioluminate.antibody.search_results_table.TableView: A table view for both full and split search results.
        
        schrodinger.ui.qt.structtable.ViewerTable
        
        schrodinger.application.combiglide.combenumdock.editableViewerTable
        
        PyQt4.QtGui.QGraphicsView: QGraphicsView(QWidget parent=None) QGraphicsView(QGraphicsScene, QWidget parent=None)
        
        schrodinger.application.combiglide.combenumdock._StructView
        
        schrodinger.ui.sketcher.sketcherView
        
        schrodinger.ui.qt.structure2d.structure_view: View which holds a structure_item object
        
        schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView: This class is a subclass of a QGraphicsView that holds a single structure_item, to display a single 2D structure.
        
        schrodinger.application.matsci.reordergui.StructureView: View which holds a structure_item object
        
        PyQt4.QtGui.QLabel: QLabel(QWidget parent=None, Qt.WindowFlags flags=0) QLabel(QString, QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.application.desmond.cwidget.AdvLabel: A mutli-line label with small, bold text.
        
        schrodinger.application.desmond.fep_gui.AdvLabel: A mutli-line label with small, bold text.
        
        schrodinger.application.bioluminate.pml_menus.ColorLabel: A label that shows off the color each element will be colored if this menu item is chosen.
        
        PyQt4.QtGui.QSplitter: QSplitter(QWidget parent=None) QSplitter(Qt.Orientation, QWidget parent=None)
        
        schrodinger.ui.sequencealignment.sequence_viewer.SequenceViewer: The sequence viewer widget displays and manipulates sequences and associated data.
        
        schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer: Creates a sequence viewer that can be opened by an action or added to a main window as a dockable item.
        
        schrodinger.application.matsci.qualityslider.QualitySlider: A widget that allows the user to see and edit the Jaguar keywords for three different accuracy levels.
        
        schrodinger.application.matsci.reordergui.ReorderAtomFrame: A frame which allows the user to reorder the atoms of a comparison structure based on the atom order of a reference structure.
        
        schrodinger.application.bioluminate.protein_report_widget.ReportFrame: A QtGui.QFrame that contains a Protein Report
        
        schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart: A Protein Report widget that can deal with multiple protein structures and also has a slider chart that can be used to select residues.
        
        schrodinger.application.bioluminate.pml_menus.ResultsWindow
        
        schrodinger.application.bioluminate.sliderchart.SliderPlot: A chart that contains four lines the user can slide to select a region of the chart.
        
        schrodinger.application.matsci.reordergui.StructureFrame: A QFrame that contains a 2D image of a structure.
        
        schrodinger.application.matsci.reordergui.ComparisonFrame: The StructureFrame for the Comparison structure
        
        schrodinger.application.matsci.reordergui.ReferenceFrame: The StructureFrame for the Reference structure
        
        PyQt4.QtGui.QGroupBox: QGroupBox(QWidget parent=None) QGroupBox(QString, QWidget parent=None)
        
        schrodinger.application.desmond.gui.AtomGroupFrame: Frame for the "Atom group" box of the Misc tab of the Advanced Options dialog.
        
        schrodinger.application.desmond.gui.InputGroup: Group Frame for showing the widgets for loading the system model.
        
        schrodinger.application.desmond.gui.MinOutputFrame: Group box "Output" of the "Minimization" tab of Advanced Options dialog.
        
        schrodinger.application.desmond.gui.MinimizerFrame: Group box "Minimizer" of the "Minimization" tab of Advanced Options dialog.
        
        schrodinger.application.desmond.gui.RandVelFrame: Frame for the "Randomize velocities" group of the Misc tab of Advanced dialog.
        
        schrodinger.application.desmond.gui._BaseGroup: Enherited by MdGroup and MinimizeGroup, so therefore by all Simulation frames
        
        schrodinger.application.desmond.gui.MdGroup: Molecular Dynamics group
        
        schrodinger.application.desmond.fep_gui._ProtItem: Frame for each checkable group of the second tab of the panel (Plan Calculation).
        
        schrodinger.application.desmond.cwidget._SdIncorpFrame: The incorporation (output) frame of the start dialog.
        
        schrodinger.application.desmond.cwidget._SdJobFrame: Frame for the master job options
        
        schrodinger.application.desmond.cwidget._SdMasterjob
        
        schrodinger.application.desmond.cwidget._SdSubjobFrame
        
        PyQt4.QtGui.QLineEdit: QLineEdit(QWidget parent=None) QLineEdit(QString, QWidget parent=None)
        
        schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit: A line edit that can be used to select a basis set.
        
        schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetEditor: A version of the BasisSelectorLineEdit that automatically sets the vertical placement of the pop up based on the constraints of the table size.
        
        schrodinger.application.bioluminate.bwidgets.NumericLineEdit: A QtGui.QLineEdit with a builtin validator for floats or integers.
        
        schrodinger.ui.qt.swidgets.SLineEdit: A QLineEdit that accepts a validator as one of its arguments
        
        schrodinger.application.matsci.atomicsymbolsgui.ElementEdit: A QLineEdit that only accepts atomic symbols and always contains the last valid value when it loses keyboard focus
        
        schrodinger.ui.qt.swidgets.SLabeledEdit: An SLineEdit that has a label attached to it.
        
        schrodinger.application.matsci.qualityslider.KeywordEdit: A swidgets.SLabeledEdit for displaying, editing and retrieving Jaguar keywords.
        
        PyQt4.QtGui.QMainWindow: QMainWindow(QWidget parent=None, Qt.WindowFlags flags=0)
        
        schrodinger.ui.qt.appframework.AppFramework: The AppFramework class is basically a hull for applications.
        
        schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog: A class which displays a dialog with a plot of the statistics for the most recent clustering
        
        schrodinger.application.canvas.clustergui.DendrogramPlotDialog: A class which displays a dialog with a plot of the dendrogram from the most recent clustering
        
        schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog: A class which displays a dialog with a plot of the distance matrix associated with the most recent clustering
        
        schrodinger.application.desmond.gui_v2.GuiApp: Base class of several Desmond panel GUI's (see its subclasses below).
        
        schrodinger.application.desmond.gui.GuiApp: Base class of several Desmond panel GUI's (see its subclasses below).
        
        schrodinger.application.moldescriptors.gui.MainUI: Launching the appframework for the GUI.
        
        schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer: The Main Panel Class
        
        schrodinger.ui.chooseligand.TestApp: Class for testing this module.
        
        schrodinger.application.desmond.fep_gui._App: Class shared by Desmond and Mcpro applications
        
        schrodinger.application.desmond.fep_gui.DesmondApp: Class shared by all Desmond panels.
        
        schrodinger.application.desmond.fep_gui.McproApp: Class shared by all Mcpro panels
        
        schrodinger.application.jaguar.gui.edit_dialog.EditDialog: A dialog that allows JaguarInput objects to be directly edited.
        
        schrodinger.application.bioluminate.ssv.viewer.ViewerWindow: Provides the SimplifiedSequenceViewer with a window to occupy.
        
        schrodinger.ui.sketcher.sketcher
        
        PyQt4.QtGui.QMenu: QMenu(QWidget parent=None) QMenu(QString, QWidget parent=None)
        
        schrodinger.application.bioluminate.pml_menus.ColorByElementSubMenu: The Color by Element submenu
        
        schrodinger.application.bioluminate.pml_menus.PMLMenu: The base menu class we subclass from
        
        schrodinger.application.bioluminate.pml_menus.ActionMenu: The Action menu
        
        schrodinger.application.bioluminate.pml_menus.AroundExpandSubMenu: The modify-around submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.AsMenu: The Show->As submenu
        
        schrodinger.application.bioluminate.pml_menus.AutoColorSubMenu: The Color menu
        
        schrodinger.application.bioluminate.pml_menus.ColorChainSubMenu: The ColorChainSubMenu menu
        
        schrodinger.application.bioluminate.pml_menus.ColorMenu: The Color menu
        
        schrodinger.application.bioluminate.pml_menus.ColorSpectrumSubMenu: The ColorSpectrumSubMenu menu
        
        schrodinger.application.bioluminate.pml_menus.ColorSubstructureSubMenu: The ColorSubstructureSubMenu menu
        
        schrodinger.application.bioluminate.pml_menus.CompleteSubMenu: The modify-complete submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.ComputeSubMenu: The Action Compute submenu
        
        schrodinger.application.bioluminate.pml_menus.EntrySubMenu: A submenu that lists all enabled Entry objects
        
        schrodinger.application.bioluminate.pml_menus.ExcludeSubMenu: The modify-exclude submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.ExtendSubMenu: The modify-extend submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.FindPCSubMenu: The Find Polar Contacts submenu
        
        schrodinger.application.bioluminate.pml_menus.GenSelectionSubMenu: The Action Generate Selection submenu
        
        schrodinger.application.bioluminate.pml_menus.GenSymMatesSubMenu: The Action Generate Symmetry Mates submenu
        
        schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu: The submenu that contains all the main actions used for most context menus
        
        schrodinger.application.bioluminate.pml_menus.ObjectFreeContextSubMenu: The GeneralContextSubMenu for a right-click that is not on an object
        
        schrodinger.application.bioluminate.pml_menus.SubstructureContextSubMenu: The GeneralContextSubMenu for a right-click that is on an atom
        
        schrodinger.application.bioluminate.pml_menus.GenerateSubMenu: The Action Generate submenu
        
        schrodinger.application.bioluminate.pml_menus.HideHydrogenSubMenu: The Hide Hydrogen submenu
        
        schrodinger.application.bioluminate.pml_menus.HideMenu: The Hide menu
        
        schrodinger.application.bioluminate.pml_menus.HydrogenSubMenu: The Action Hydrogen submenu
        
        schrodinger.application.bioluminate.pml_menus.IncludeSubMenu: The modify-include submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.InvertSubMenu: The modify-invert submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.LabelAtomIdentSubMenu: The Label Atom Identifiers submenu
        
        schrodinger.application.bioluminate.pml_menus.LabelMenu: The Label menu
        
        schrodinger.application.bioluminate.pml_menus.LabelOtherSubMenu: The Label Other Properties submenu
        
        schrodinger.application.bioluminate.pml_menus.LigandSitesSubMenu: The Action-Preset-Ligand Sites submenu
        
        schrodinger.application.bioluminate.pml_menus.ModifySubMenu: The modify submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.PMLContextMenu: The base menu class we subclass from for context menus
        
        schrodinger.application.bioluminate.pml_menus.AtomContextMenu: The context menu for right-clicks on non-selected atoms
        
        schrodinger.application.bioluminate.pml_menus.SelectedAtomContextMenu: The context menu for right-clicks on selected atoms
        
        schrodinger.application.bioluminate.pml_menus.SpaceContextMenu: The context menu for right-clicks in space
        
        schrodinger.application.bioluminate.pml_menus.PolarContactsSubMenu: The Polar Contacts submenu
        
        schrodinger.application.bioluminate.pml_menus.PresetSubMenu: The Preset submenu
        
        schrodinger.application.bioluminate.pml_menus.RestrictSubMenu: The modify-restrict submenu of the action menu
        
        schrodinger.application.bioluminate.pml_menus.SelectedAtomContextActionSubMenu: The submenu that allows the user to enable/disable individual objects
        
        schrodinger.application.bioluminate.pml_menus.SelectionSubMenu: A submenu that lists all enabled Entry objects
        
        schrodinger.application.bioluminate.pml_menus.ShowMenu: The Show menu
        
        schrodinger.application.bioluminate.pml_menus.SurfaceAreaSubMenu: The Action Surface Area submenu
        
        schrodinger.application.bioluminate.pml_menus.ToggleStateSubMenu: The submenu that allows the user to enable/disable individual objects
        
        schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu: A submenu that shows the most recently chosen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.RecentCarbonColorSubMenu: A submenu that shows the most recently chosen carbon colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.RecentHydrogenColorSubMenu: A submenu that shows the most recently chosen hydrogen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.RecentObjectColorSubMenu: A submenu that shows the most recently chosen object colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.
        
        schrodinger.application.bioluminate.pml_menus.ShowOrganicMenu: The Show->Organic submenus
        
        schrodinger.application.bioluminate.pml_menus.ShowSubstructureMenu: The Show->substructure submenus
        
        PyQt4.QtGui.QToolBar: QToolBar(QString, QWidget parent=None) QToolBar(QWidget parent=None)
        
        schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar: Get the toolbar that has the combobox with the antibody numering schemes.
        
        schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar: A toolbar associated with the viewer that will handle display options.
        
        schrodinger.application.bioluminate.ssv.toolbars.FindToolBar: Create an instance of the "Find Pattern" toolbar from the MSV.
        
        schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar: Get the toolbar that has the import dialogs.
        
        schrodinger.ui.sketcher.sketcherGUIMultiColumnToolBar
        
        schrodinger.application.moldescriptors.gui.QikPropUI
        
        schrodinger.application.desmond.gui.RelaxFrame: Frame that includes the "Relax model..." check box and the relaxation protocol entry field.
        
        schrodinger.application.desmond.gui.RestraintsTab: Frame for the Restraints tab of the Advanced Options dialog
        
        schrodinger.application.bioluminate.bwidgets.RowActionItem: Custom widget to be used in a table cell.
        
        schrodinger.application.desmond.gui.SimOptionsFrame: Responsible for drawing the simulation options widgets, including Simulation time and Recording intervals.
        
        schrodinger.application.jaguar.gui.theory_tab_widgets.SpinRestrictedWidget: This widget allows user to specify SCF spin treatment options.
        
        schrodinger.application.bioluminate.antibody.search_results_table.SplitTable: A widget to contain both split search results tables (i.e.
        
        schrodinger.application.desmond.fep_gui._DesmondProt: Frame for the second tab ("Plan Calculation") of the Desmond GUIs.
        
        schrodinger.application.desmond.fep_gui._McproProt: Frame for the second tab ("Plan Calculation") of the Mcpro GUIs.
        
        schrodinger.application.desmond.fep_gui._Pert: Frame for the bottom part of the "Plan Calculation" tab of Mcpro GUIs.
        
        schrodinger.application.desmond.cwidget._SdDetailFrame: Frame for the section that gets shown when the "Detail" button is toggled on.
      - schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant: This class holds all the information for each participant in the reaction, be it reactant or product.
      - schrodinger.application.combiglide.combenumdock.SimpleEnumDockPanel: This is the main class for the panel, to show the panel simply create an instance of this class.
      - schrodinger.application.jaguar.gui.basis_selector._BasisSelectorPopUpEventFilter: An event filter that will hide the _BasisSelectorPopUp when appropriate
    - schrodinger.ui.sketcher.sketcherMolecule
- tuple: tuple() -> empty tuple tuple(iterable) -> tuple initialized from iterable's items
  - schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple: ProjEntryTuple(struc, charge, spin_mult, basis)
  - schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka: ProjEntryTuplePka(struc, charge, spin_mult, pka_atom)
  - schrodinger.application.jaguar.gui.tabs.solvation_tab.Solvent: Solvent(name, keyvalue, dielectric, radius, weight, density)
  - schrodinger.application.jaguar.gui.input_tab_widgets._Basis: Basis(basis, polarization, diffuse)
    - schrodinger.application.jaguar.gui.input_tab_widgets.Basis: Class for representing a basis set.
  - schrodinger.application.jaguar.basis._BasisSet: BasisSet(name, backup, nstar, nplus, is_ecp, is_ps, numd, numf)
    - schrodinger.application.jaguar.basis.BasisSet: A Pythonic wrapper for basis set information.
- type: type(object) -> the object's type type(name, bases, dict) -> a new type
  - abc.ABCMeta: Metaclass for defining Abstract Base Classes (ABCs).
  - schrodinger.application.desmond.ffiostructure._FEPIOSubBlockMeta: A meta-class to different fepio sub block type classses.
  - schrodinger.application.desmond.ffiostructure._FFIOSubBlockMeta: A meta-class to different ffio sub block type classses.
  - schrodinger.application.desmond.picklejar.Picklable.__metaclass__
    - schrodinger.application.desmond.cmj.StageBase.__metaclass__
  - schrodinger.application.desmond.systype.TyperBase.__metaclass__
schrodinger.application.mcpro.zmat.proteinHandler: Class provides methods to write the pepz input file
schrodinger.ui.widget.pmwwidget.schroPmwWrapper: Parent class for all Schrodinger Pmw widgets.
- schrodinger.ui.widget.pmwwidget.Balloon: Class that mimics the Pmw.Balloon class.
- schrodinger.ui.widget.pmwwidget.ButtonBox: Class that mimics the Pmw.ButtonBox class.
- schrodinger.ui.widget.pmwwidget.ComboBox: Class that mimics the Pmw.ComboBox class.
  - schrodinger.ui.propertyselector.PropertySelectorMenu: Pull-down menu style property selected Used by VSW GUI
- schrodinger.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.ui.macromodel.AsetFrame: A graphical component to set up Atom Set Interaction (ASET) jobs in MacroModel.
  - schrodinger.application.mcpro.guide.Guide: This class provides a simplistic workflow widget.
  - schrodinger.application.desmond.guide.Guide: This class provides a primitive workflow widget.
  - schrodinger.ui.appframework.JobInputFrame: An application input source selection widget.
    - schrodinger.ui.appframework.AppJobInputFrame: A JobInputFrame that provides the setup method for use in the AppFramework class.
    - schrodinger.ui.appframework.MultiInputFrame: A JobInputFrame that can handle multiple file selections.
  - schrodinger.ui.macromodel.LoopFrame: A GUI component to support setting up of LOOP loop searching jobs in MacroModel.
  - schrodinger.ui.macromodel.MiniFrame: A frame which provides controls to setup a MacroModel minimization job.
  - schrodinger.ui.macromodel.PotentialFrame: A Potential Energy Surface description widget.
  - schrodinger.ui.propertyselector.PropertySelector: Class for selecting properties, with features to organize by family/owner, filter by name, and/or sort items in the list.
  - schrodinger.ui.macromodel.SbcFrame: A file selection widget for selecting substructure (*.sbc) files.
  - schrodinger.application.desmond.guide._Step: This is a class that represents the step as in the 'guide' widget (see below).
- schrodinger.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.