Module Hierarchy

_licensing'
_mmutil'
_phase'
_pyepik'
_structure'
schrodinger: This is the top level package for all Schrodinger modules.
- schrodinger.analysis: A package for analysis modules.
  - schrodinger.analysis.enrichment: A module for calculating Enrichment Factors and reporting on the effectiveness of a ligand database screen seeded with known actives.
  - schrodinger.analysis.visanalysis: Molecular structures reside in a three-dimensional world and naturally enough give rise to three-dimensional data.
- schrodinger.application: A package for application specific modules.
  - schrodinger.application.aacg
    - schrodinger.application.aacg.utils: Utilities for working with aacg-related files.
  - schrodinger.application.bioluminate: BioLuminate specific functionality
    - schrodinger.application.bioluminate.actions
      - schrodinger.application.bioluminate.actions.configs: Contains configuration options specific to BioLuminate actions.
      - schrodinger.application.bioluminate.actions.factory: Contains Qt actions specific to the BioLuminate application.
      - schrodinger.application.bioluminate.actions.icons: Contains icons specific to BioLuminate.
    - schrodinger.application.bioluminate.antibody
      - schrodinger.application.bioluminate.antibody.management: Module for tools to manage the antibody database
      - schrodinger.application.bioluminate.antibody.search_results_table: Classes for the search results table used in the Antibody Prediction and Antibody Humanization: CDR Grafting panels.
      - schrodinger.application.bioluminate.antibody.utils: Useful classes and functions for working with Antibodies
    - schrodinger.application.bioluminate.antibody_utils: Useful classes and functions for working with Antibodies
    - schrodinger.application.bioluminate.bwidgets: Collection of widgets common to multiple BioLuminate panels.
    - schrodinger.application.bioluminate.pml_menus: The module that creates the actions and menus for the Pymol-like interface of BioLuminate.
    - schrodinger.application.bioluminate.propfilter: This contains a QDialog class that allows the user to define criteria to filter properties by.
    - schrodinger.application.bioluminate.propfilter_ui
    - schrodinger.application.bioluminate.propka_parse: Module used to parse the output from a propka job.
    - schrodinger.application.bioluminate.protein: Module to gather residue property data for proteins.
    - schrodinger.application.bioluminate.protein_report_widget
    - schrodinger.application.bioluminate.protein_structure_quality
    - schrodinger.application.bioluminate.protein_structure_quality_ui
    - schrodinger.application.bioluminate.run_propka: PROPKA wrapper functions
    - schrodinger.application.bioluminate.sliderchart: Tools for using matplotlib charts.
    - schrodinger.application.bioluminate.ssv: BioLuminate Sequence Viewer functionality
      - schrodinger.application.bioluminate.ssv.toolbars: Toolbars for the SimplifiedSequenceViewer
      - schrodinger.application.bioluminate.ssv.viewer: The simplified version of the sequence viewer used in the MSV.
    - schrodinger.application.bioluminate.surfcomp: See PYTHON-2433 WARNING: Solvents are not accounted for in any way.
    - schrodinger.application.bioluminate.validate_imported_modules: The module will check that the psp module is loaded
    - schrodinger.application.bioluminate.workspacelabeler
  - schrodinger.application.canvas: A package that contains Canvas functionality.
    - schrodinger.application.canvas.base: Base python wrappers to the Canvas C++ libraries.
    - schrodinger.application.canvas.cluster: Canvas clustering functionality.
    - schrodinger.application.canvas.clustergui
    - schrodinger.application.canvas.driverutils: Utility functions for writing Canvas drivers in python.
    - schrodinger.application.canvas.fingerprint: Higher-level wrappers to the Canvas Fingerprint generation and manipulation classes.
    - schrodinger.application.canvas.fingerprintgui
    - schrodinger.application.canvas.r_group: Detect r-groups from CanvasMCS, CombiGlide, or SMARTS
    - schrodinger.application.canvas.r_group_dee: R-Group Analysis Dead End elimination
    - schrodinger.application.canvas.similarity: Support for Canvas fingerprint similarity operations.
    - schrodinger.application.canvas.similaritygui
    - schrodinger.application.canvas.utils: Canvas utility functions.
  - schrodinger.application.combiglide: Package containing CombiGlide functionality
    - schrodinger.application.combiglide.combenumdock: Creates the Combiglide Interactive Enumeration and Dock panel.
    - schrodinger.application.combiglide.combenumdock_dir
    - schrodinger.application.combiglide.connection_storage
    - schrodinger.application.combiglide.corehop: This module contains classes and functions for Core Hopping.
    - schrodinger.application.combiglide.packages: Package for CombiGlide specific modules installed with the CombiGlide product.
      - schrodinger.application.combiglide.packages.chutils
      - schrodinger.application.combiglide.packages.core_classifier: A module to provide a core classification for use with the the core_partitionifiction module.
      - schrodinger.application.combiglide.packages.hierarchy: A module to navigate a particular type of hierarchy.
    - schrodinger.application.combiglide.utils: This module contains the utility functions for CombiGlide.
  - schrodinger.application.desmond: Desmond-related modules.
    - schrodinger.application.desmond.ana: Tools for various Desmond-related analyses.
    - schrodinger.application.desmond.antlr3: @package antlr3 @brief ANTLR3 runtime package
      - schrodinger.application.desmond.antlr3.compat: Compatibility stuff
      - schrodinger.application.desmond.antlr3.constants: ANTLR3 runtime package
      - schrodinger.application.desmond.antlr3.debug
      - schrodinger.application.desmond.antlr3.dfa: ANTLR3 runtime package
      - schrodinger.application.desmond.antlr3.dottreegen: @package antlr3.dottreegenerator @brief ANTLR3 runtime package, tree module
      - schrodinger.application.desmond.antlr3.exceptions: ANTLR3 exception hierarchy
      - schrodinger.application.desmond.antlr3.extras: @package antlr3.dottreegenerator @brief ANTLR3 runtime package, tree module
      - schrodinger.application.desmond.antlr3.main: ANTLR3 runtime package
      - schrodinger.application.desmond.antlr3.recognizers: ANTLR3 runtime package
      - schrodinger.application.desmond.antlr3.streams: ANTLR3 runtime package
      - schrodinger.application.desmond.antlr3.tokens: ANTLR3 runtime package
      - schrodinger.application.desmond.antlr3.tree: @package antlr3.tree @brief ANTLR3 runtime package, tree module
      - schrodinger.application.desmond.antlr3.treewizard: @package antlr3.tree @brief ANTLR3 runtime package, treewizard module
    - schrodinger.application.desmond.autopartition: A module to provide multiset partition, combination and processor topology decomposition.
    - schrodinger.application.desmond.cmj: This module provides fundamental facilities for writing a multisim driver script, for writing multisim concrete stage classes, and for dealing with protocol files.
    - schrodinger.application.desmond.cms: Classes and functions for dealing with *.cms files.
    - schrodinger.application.desmond.cns_io
    - schrodinger.application.desmond.config: Utilities for handling Desmond config files.
    - schrodinger.application.desmond.correlation_tau: This program computes the average correlation coefficient and the kendall tau rank coefficient between experiment and prediction samples.
    - schrodinger.application.desmond.cwidget: Widgets used mainly in Desmond and MCPRO+ panels.
    - schrodinger.application.desmond.deltaE
    - schrodinger.application.desmond.desmond_advanced_tab_ui
    - schrodinger.application.desmond.destro
    - schrodinger.application.desmond.energygroup: Module for calculating and retriving energy components from Desmond's vrun program.
    - schrodinger.application.desmond.enhanced_sampling
      - schrodinger.application.desmond.enhanced_sampling.FcnTypes
      - schrodinger.application.desmond.enhanced_sampling.mexpLexer
      - schrodinger.application.desmond.enhanced_sampling.mexpParser
    - schrodinger.application.desmond.enhsamp
    - schrodinger.application.desmond.envir: Commonly used Desmond environment variables.
    - schrodinger.application.desmond.event_analysis: This module is for code that's shared between the event analysis panel and the Materials Science event analysis panel
      - schrodinger.application.desmond.event_analysis.pl_image_tools
    - schrodinger.application.desmond.fep_edge_data
    - schrodinger.application.desmond.fep_edge_report_maker
    - schrodinger.application.desmond.fep_gui: A FEP setup panel that supports both the Desmond and the MCPRO+ simulation engines.
    - schrodinger.application.desmond.fep_mapping
    - schrodinger.application.desmond.fep_net_charge
    - schrodinger.application.desmond.fep_reporter
    - schrodinger.application.desmond.fep_scholar_msj_generator
    - schrodinger.application.desmond.fep_scholar_rules
    - schrodinger.application.desmond.fep_scholar_util
    - schrodinger.application.desmond.fep_struc: Defines a `Struc' class as a generic represention of molecular structure
    - schrodinger.application.desmond.fep_util
    - schrodinger.application.desmond.fepana: Tools for various FEP-related analyses.
    - schrodinger.application.desmond.fepdiff: A module to compare various block of mmffio and mmfepio blocks.
    - schrodinger.application.desmond.feputils
    - schrodinger.application.desmond.ffiostructure
    - schrodinger.application.desmond.gaussian_filter: Create and filter 3D histogram with gaussian function.
    - schrodinger.application.desmond.gchart: Tools for using google chart.
    - schrodinger.application.desmond.gconfig: Utilities for handling gDesmond config files.
    - schrodinger.application.desmond.gui
    - schrodinger.application.desmond.guide: A primitive workflow widget called Guide.
    - schrodinger.application.desmond.icon: Various panels for FEP calculations for Desmond applications.
    - schrodinger.application.desmond.input_group_ui
    - schrodinger.application.desmond.maestro: A collection of numerous useful functions and classes for working with Maestro.
    - schrodinger.application.desmond.mapper_msj_generator
    - schrodinger.application.desmond.mdkey: Functions for initializing, reading, and writing Desmond parameters.
    - schrodinger.application.desmond.mdpose
      - schrodinger.application.desmond.mdpose.mdpose_analysis
      - schrodinger.application.desmond.mdpose.mdpose_average_structure
      - schrodinger.application.desmond.mdpose.mdpose_glide
      - schrodinger.application.desmond.mdpose.mdpose_neutralize
      - schrodinger.application.desmond.mdpose.mdpose_strain_energy
      - schrodinger.application.desmond.mdpose.mdposejob
    - schrodinger.application.desmond.measurement: A class for simple arithmetic with uncertainty.
    - schrodinger.application.desmond.memory_estimate
    - schrodinger.application.desmond.meta: Module for all metadynamics backend functionality
    - schrodinger.application.desmond.mplchart: Tools for using matplotlib charts.
    - schrodinger.application.desmond.multisimstartup
    - schrodinger.application.desmond.picklejar: Facilities for pickling objects that are otherwise uneasy to pickle, e.g., class attributes.
    - schrodinger.application.desmond.predict_remd_temp: A script for predicting temperature profile for REMD simulations.
    - schrodinger.application.desmond.r_group_asl
    - schrodinger.application.desmond.remd: Utilities for REMD.
    - schrodinger.application.desmond.reorder_atom: Functions to reorder atoms.
    - schrodinger.application.desmond.repair_cms
    - schrodinger.application.desmond.replica_dE
    - schrodinger.application.desmond.replica_exchange_review
    - schrodinger.application.desmond.replica_sid_generator
    - schrodinger.application.desmond.report_helper
    - schrodinger.application.desmond.rest_inp
    - schrodinger.application.desmond.rest_tab_ui
    - schrodinger.application.desmond.simulation_block_data: Block data calculation script.
    - schrodinger.application.desmond.simulation_block_test: Block data analysis script.
    - schrodinger.application.desmond.smarts: SMARTS matching utility using MMPATTY.
    - schrodinger.application.desmond.stage: Various multisim concrete stage classes.
    - schrodinger.application.desmond.starter: Copyright Schrodinger, LLC.
      - schrodinger.application.desmond.starter.generator: Copyright Schrodinger, LLC.
        
        schrodinger.application.desmond.starter.generator.fep_plus
      - schrodinger.application.desmond.starter.starter: Command line helper
      - schrodinger.application.desmond.starter.ui: Copyright Schrodinger, LLC.
        
        schrodinger.application.desmond.starter.ui.cmdline: Starter backbone
        
        schrodinger.application.desmond.starter.ui.fep_plus
        
        schrodinger.application.desmond.starter.ui.multisim
    - schrodinger.application.desmond.struc: A collection of miscellaneous molecular-structure-related functions.
    - schrodinger.application.desmond.system_builder_inp: A script to create a system builder input file.
    - schrodinger.application.desmond.system_builder_util
    - schrodinger.application.desmond.systype: Facilities for detecting type of model systems.
    - schrodinger.application.desmond.title_to_hex: This map can be displayed by using the --pkl_name option before launching to see what edges in the graph are available for extension.
    - schrodinger.application.desmond.util: Utility functions and classes that may make your coding life easier and cleaner.
    - schrodinger.application.desmond.xvfbwrapper: wrapper for running display inside X virtual framebuffer (Xvfb)
  - schrodinger.application.epik
    - schrodinger.application.epik.pyepik: Epik
  - schrodinger.application.glide: Glide-related modules.
    - schrodinger.application.glide.ensemble_selection: Classes for representing receptor ensembles and for choosing the best ensembles of a specified size from a cross-docking experiment.
    - schrodinger.application.glide.glide
    - schrodinger.application.glide.glideanalysis: Functions and classes for calculating Glide Docking Enrichment Factors and creating sorted pose libraries.
    - schrodinger.application.glide.gui
    - schrodinger.application.glide.http_client: Glide HTTP client
    - schrodinger.application.glide.http_server: Glide HTTP Server
    - schrodinger.application.glide.liaison_lsbd
    - schrodinger.application.glide.poseviewconvert: Functions for creating or converting pose viewer files.
    - schrodinger.application.glide.utils: Glide utility functions.
    - schrodinger.application.glide.xpdes: Classes for reading and writing Glide XP Descriptor (.xpdes) files.
  - schrodinger.application.inputconfig: A modified version of the configobj module.
  - schrodinger.application.jaguar: Jaguar-related modules.
    - schrodinger.application.jaguar.basis: Utility functions for dealing with Jaguar basis sets
    - schrodinger.application.jaguar.check_headers_mod
    - schrodinger.application.jaguar.constants: Constants used in unit conversion.
    - schrodinger.application.jaguar.gui
    - schrodinger.application.jaguar.input: Functions and classes for reading and creating Jaguar input files.
    - schrodinger.application.jaguar.jaguar_keyword_utils
    - schrodinger.application.jaguar.keywordDB
    - schrodinger.application.jaguar.make_headers_mod
    - schrodinger.application.jaguar.mmjag: A wrapper to the C mmjag functions.
    - schrodinger.application.jaguar.output: Classes for parsing Jaguar output files and accessing output properties programmatically.
    - schrodinger.application.jaguar.rmsd: This module is a subclass of schrodinger.structutils.rmsd to provide ability to do searching over more permutations of possible renumbering.
    - schrodinger.application.jaguar.scan: Support functions and classes for Jaguar scans.
    - schrodinger.application.jaguar.utils: Jaguar utility functions.
    - schrodinger.application.jaguar.validation: Jaguar keywords input validation and specialized exceptions
  - schrodinger.application.licensing: Licensing-related modules.
    - schrodinger.application.licensing.flexlm
    - schrodinger.application.licensing.licadmin
    - schrodinger.application.licensing.licerror
  - schrodinger.application.ligprep: LigPrep related modules.
    - schrodinger.application.ligprep.ionizer
  - schrodinger.application.macromodel: MacroModel-related modules.
    - schrodinger.application.macromodel.apps: Functions that combine macromodel.utils and macromodel.tools to create mini-applications and workflows.
    - schrodinger.application.macromodel.input: Facilities for reading and writing simplified MacroModel input files.
    - schrodinger.application.macromodel.paraUtils
    - schrodinger.application.macromodel.tools: Useful functions for setting up MacroModel jobs.
    - schrodinger.application.macromodel.utils: Utilities for writing MacroModel com, sbc, and hst (native input) files.
  - schrodinger.application.matsci: Materials Science functionality
    - schrodinger.application.matsci.amorphous
    - schrodinger.application.matsci.atomicsymbols: The full set of atomic symbols and characters that begin atomic symbols.
    - schrodinger.application.matsci.atomicsymbolsgui
    - schrodinger.application.matsci.basiselements
    - schrodinger.application.matsci.buildcomplex
    - schrodinger.application.matsci.builderwidgets
    - schrodinger.application.matsci.desmondutils
    - schrodinger.application.matsci.enumeration
    - schrodinger.application.matsci.genetic_optimization: Genetic optimization module.
      - schrodinger.application.matsci.genetic_optimization.genetic_optimization
    - schrodinger.application.matsci.jaguarworkflows
    - schrodinger.application.matsci.jobutils
    - schrodinger.application.matsci.msicons
      - schrodinger.application.matsci.msicons.controlicons
    - schrodinger.application.matsci.mswidgets
    - schrodinger.application.matsci.nano: Nanostructure module.
      - schrodinger.application.matsci.nano.check
      - schrodinger.application.matsci.nano.constants: Constants for building nanostructures.
      - schrodinger.application.matsci.nano.interface_mod
      - schrodinger.application.matsci.nano.particle
      - schrodinger.application.matsci.nano.plane
      - schrodinger.application.matsci.nano.sheet
      - schrodinger.application.matsci.nano.slab
      - schrodinger.application.matsci.nano.surfaces_interfaces_mod
      - schrodinger.application.matsci.nano.tube
      - schrodinger.application.matsci.nano.util
      - schrodinger.application.matsci.nano.xtal
    - schrodinger.application.matsci.optoelectronics: Constants and other commonly used optoelectronics objects
    - schrodinger.application.matsci.property_names: Constants for CT-level Materials Science properties.
    - schrodinger.application.matsci.qualityslider: A QSlider that allows the user to select Jaguar keywords based on Coarse/Medium/Accurate settings.
    - schrodinger.application.matsci.reorder: Creates a frame that contains widgets to aid in reordering two structures to have the same atom order, plus functions to estimate atom ordering.
    - schrodinger.application.matsci.reordergui: This module contains classes to enable use of the reorder module in a GUI.
    - schrodinger.application.matsci.rxn_channel: Reaction channel module.
      - schrodinger.application.matsci.rxn_channel.rxn_channel
    - schrodinger.application.matsci.rxn_path
    - schrodinger.application.matsci.shapes
    - schrodinger.application.matsci.spectra
    - schrodinger.application.matsci.textlogger
    - schrodinger.application.matsci.zmutils
  - schrodinger.application.mcpro: MCPRO+ modules.
    - schrodinger.application.mcpro.ddg
    - schrodinger.application.mcpro.fep
    - schrodinger.application.mcpro.guide: A simple workflow widget.
    - schrodinger.application.mcpro.lrm
    - schrodinger.application.mcpro.mc
    - schrodinger.application.mcpro.mini
    - schrodinger.application.mcpro.modelsystemwizard
    - schrodinger.application.mcpro.perturbations
    - schrodinger.application.mcpro.read_output: Class to read summary/monitor file.
    - schrodinger.application.mcpro.residuetools
    - schrodinger.application.mcpro.solvent
    - schrodinger.application.mcpro.writeinputs
    - schrodinger.application.mcpro.zmat
  - schrodinger.application.medchem
    - schrodinger.application.medchem.property: Functions for computing medchem properties.
  - schrodinger.application.moldescriptors
  - schrodinger.application.mopac: MOPAC-related modules.
    - schrodinger.application.mopac.mopac_api: This is the top-level interface for running MOPAC calculations with Schrodinger python scripts.
    - schrodinger.application.mopac.mopac_launchers: This module contains classes for launching different MOPAC versions.
    - schrodinger.application.mopac.mopac_results: This is for parsing output from different MOPAC versions.
    - schrodinger.application.mopac.results2012: This module parses and stores the results of a MOPAC2012 calculation.
    - schrodinger.application.mopac.results71: A module to parse and store the results of a MOPAC7.1 calculation.
    - schrodinger.application.mopac.structure_launchers: Currently, we assume this code is universal for all versions of MOPAC we support.
    - schrodinger.application.mopac.utils
  - schrodinger.application.msv
    - schrodinger.application.msv.msv_menu: Holds the list of all menu information including menu names, menu option names, slots, tool tips, short cuts, and child lists.
  - schrodinger.application.phase: Phase-related modules.
    - schrodinger.application.phase.hypothesis: Module for reading and writing Phase hypotheses.
    - schrodinger.application.phase.phase_markers
  - schrodinger.application.prepwizard: Shared functionality between PrepWizard GUI and command-line PrepWizard.
  - schrodinger.application.prime: Modules for dealing with Prime.
    - schrodinger.application.prime.gui
      - schrodinger.application.prime.gui.analyze_energy
      - schrodinger.application.prime.gui.ui
        
        schrodinger.application.prime.gui.ui.analyze_energy_ui
        
        schrodinger.application.prime.gui.ui.environment_options_ui
    - schrodinger.application.prime.input: A class for reading and writing Prime simplified input files.
    - schrodinger.application.prime.primefix: Functions and classes for Prime molecule preparation.
    - schrodinger.application.prime.residue_interaction: A Python interface to Prime residue interaction data
  - schrodinger.application.qsite: Modules for working with QSite.
    - schrodinger.application.qsite.input: Module for reading and writing QSite input files.
    - schrodinger.application.qsite.output: A class for parsing of QSite output files.
  - schrodinger.application.report2d: Utilities for generating PDF and HTML 2D report files.
  - schrodinger.application.ska: Core routines for wrapping SKA backend.
  - schrodinger.application.utils: Utility functions for finding python packages in product directories.
  - schrodinger.application.vsw: Deprecated for schrodinger.pipeline
    - schrodinger.application.vsw.input
    - schrodinger.application.vsw.pipeutils
    - schrodinger.application.vsw.stages: Pipeline stage modules used by VSW and QPLD.
    - schrodinger.application.vsw.vswinput: Class for writing VSW (not general Pipeline) input files.
  - schrodinger.application.watermap: WaterMap-related modules.
    - schrodinger.application.watermap.utils: General WaterMap utilities
    - schrodinger.application.watermap.watermap_inp
    - schrodinger.application.watermap.watermap_scoring
- schrodinger.graphics3d: Various classes for drawing 3D objects in the Maestro workspace via OpenGL.
  - schrodinger.graphics3d.arrow: OpenGL arrows.
  - schrodinger.graphics3d.box: OpenGL boxes.
  - schrodinger.graphics3d.common: Utility functions for the graphics3d package.
  - schrodinger.graphics3d.gridbox: Module for drawing a grid box to the Workspace.
  - schrodinger.graphics3d.lines: OpenGL lines.
  - schrodinger.graphics3d.polygon: OpenGL polygons.
  - schrodinger.graphics3d.polyhedron: The polyhedron module allows creation and drawing of polyhedra.
  - schrodinger.graphics3d.quadrilateral: OpenGL quadrilaterals.
  - schrodinger.graphics3d.sphere: OpenGL spheres.
- schrodinger.infra: Infrastructure modules, including wrappers to basic mmlib types.
  - schrodinger.infra._mmgpgpu
  - schrodinger.infra._mmreflect
  - schrodinger.infra._ska
  - schrodinger.infra.ark: Python interface for Ark
  - schrodinger.infra.canvas
  - schrodinger.infra.canvas2d
  - schrodinger.infra.exception_handler: A top level exception handler that writes uncaught exceptions to a folder in .schrodinger.
  - schrodinger.infra.exception_handler_dir
    - schrodinger.infra.exception_handler_dir.exception_dialog
    - schrodinger.infra.exception_handler_dir.exception_dialog_ui
  - schrodinger.infra.licensing: See schrodinger.utils.license
  - schrodinger.infra.mm: Python-level wrappers for the SWIG-wrapped C and C++ functions.
  - schrodinger.infra.mmbitset: A pythonic wrapper for the mmbs library, providing access to bitsets.
  - schrodinger.infra.mmcheck
  - schrodinger.infra.mmerr: Utility functions for the mmerr library.
  - schrodinger.infra.mmgpgpu: GPGPU utility C++ functions
  - schrodinger.infra.mmim: Wrapper classes and functions for dealing with the MMIM library, which is used to read & write Impact and QSite input files.
  - schrodinger.infra.mminit: A class to assist in initialization and termination of mmlibs.
  - schrodinger.infra.mmkv: Wrapper classes and functions for dealing with the MMKV library, which is used to read & write Epik, LigPrep, and ConfGen input files.
  - schrodinger.infra.mmlist: A wrapper for the mmlist mmlib.
  - schrodinger.infra.mmobject: A base class for creation of garbage collected, object-oriented wrappers of the mmlibs.
  - schrodinger.infra.mmproj: Python-level wrappers for the SWIG-wrapped C and C++ functions.
  - schrodinger.infra.mmreflect: C++ wrapper for x-ray reflection functionality
  - schrodinger.infra.mmsurf: C++ wrapper for surface related functionality
  - schrodinger.infra.mopac
  - schrodinger.infra.phase: Phase C++ wrappers
  - schrodinger.infra.projectmodel
  - schrodinger.infra.propedit: Support functions for Structure property manipulation functions in the propeditor script.
  - schrodinger.infra.structure
  - schrodinger.infra.table: A pythonic wrapper to an mmlibs mmtable object.
  - schrodinger.infra.util: General infrastructure level utilities.
- schrodinger.job: Functionality for running programs under Job Control and accessing Job Control features.
  - schrodinger.job.app: A base class for applications that can be run under job control.
  - schrodinger.job.host_check: This module provides functions to support hosts-file and remote-command configuration in the Configuration GUI.
  - schrodinger.job.hunt_cache: Speed up hunt with caching.
  - schrodinger.job.hunt_stub: This module support limited hunt options from original hunt.py to show entries from hosts file.
  - schrodinger.job.jobcontrol
  - schrodinger.job.launcher
  - schrodinger.job.queue: A class for running multiple concurrent jobs.
  - schrodinger.job.remote_command
  - schrodinger.job.util: Job Control utilities.
- schrodinger.maestro: Modules that allow for interaction with Maestro.
  - schrodinger.maestro.maestro: Core functions for interaction with Maestro.
  - schrodinger.maestro.markers: Module for placing markers in the Workspace.
- schrodinger.pipeline: Modules for the Pipeline mechanism used by VSW & QPLD.
  - schrodinger.pipeline.input: Classes for writing Pipeline input files.
  - schrodinger.pipeline.pipeio
  - schrodinger.pipeline.pipeline
  - schrodinger.pipeline.pipeutils
  - schrodinger.pipeline.stage
  - schrodinger.pipeline.stages: Pipeline stage modules used by VSW and QPLD.
- schrodinger.project: A module for accessing and modifying a Maestro Project.
- schrodinger.protein: Protein related modules, including functionality for analysis and manipulation.
  - schrodinger.protein._reliability
  - schrodinger.protein.analysis
  - schrodinger.protein.analysis_params
  - schrodinger.protein.assignment
  - schrodinger.protein.captermini
  - schrodinger.protein.findhets
  - schrodinger.protein.getpdb
  - schrodinger.protein.getpdb_utility
  - schrodinger.protein.helix
  - schrodinger.protein.membrane: Module for displaying and manipulating a membrane.
  - schrodinger.protein.reliability
  - schrodinger.protein.remediate: Module for remediating names in PDB structures - converting PDBv2 residue and atom names to PDBv3 convention.
  - schrodinger.protein.rotamers: A rotamer library which can be applied to protein sidechains.
  - schrodinger.protein.sequence: This module allows to iterate over all sequences in a given protein CT, and to iterate over residues of each (in sequence order).
- schrodinger.structure
- schrodinger.structutils: A package containing Schrodinger structure utility modules.
  - schrodinger.structutils.analyze: Functions for analyzing Structure objects.
  - schrodinger.structutils.assignbondorders: A module to assign bond orders based on molecular geometry.
  - schrodinger.structutils.build: Functions for modifying chemical structures.
  - schrodinger.structutils.color: An interface to the Maestro color palette and color schemes.
  - schrodinger.structutils.createfragments: This script will break up a set of input molecules into fragments based on some simple rules, similar to those described in the original RECAP paper.
  - schrodinger.structutils.interactionfp
  - schrodinger.structutils.interactions
  - schrodinger.structutils.io
  - schrodinger.structutils.measure: Functions for measuring distances and angles in structures.
  - schrodinger.structutils.minimize: A module for force field energy evaluation and minimization.
  - schrodinger.structutils.ringspear
  - schrodinger.structutils.rmsd
  - schrodinger.structutils.sitealign
  - schrodinger.structutils.smiles: A module for generating SMILES and unique SMILES strings.
  - schrodinger.structutils.smilesfilter: A group of functions and classes to help filtering structure files on unique SMILES strings.
  - schrodinger.structutils.sort: A module for sorting structure files by Structure-level property values.
  - schrodinger.structutils.structalign: A module for performing protein structure alignment.
  - schrodinger.structutils.transform: A module for manipulating atom coordinates with matrix operations.
- schrodinger.surface: Pythonic wrappings for mmsurf surfaces
- schrodinger.test
  - schrodinger.test.build_test_structures: Some convenience functions to quickly and reproducibly create structures for testing.
  - schrodinger.test.canvas_utils: Container for common test functions used in Canvas tests
  - schrodinger.test.custom_assertions: Contains custom assertions for use with unittest and Schrodinger data structures.
  - schrodinger.test.custom_test_classes: Custom test classes
  - schrodinger.test.darwinconsole
  - schrodinger.test.decorate_fflag: Enable or disable a feature flag in a specific situation.
  - schrodinger.test.get_widget_image
  - schrodinger.test.ioredirect
  - schrodinger.test.performance
    - schrodinger.test.performance.api: Base class for performance tests.
    - schrodinger.test.performance.general: General tools for performance tests.
    - schrodinger.test.performance.reporter: Basic client-side components for performance testing.
  - schrodinger.test.structurecheck: Custom assertions for "checking" structures.
  - schrodinger.test.stu
    - schrodinger.test.stu.base_executable: Base class for STU utilities.
    - schrodinger.test.stu.client: Client for communication with STU server.
    - schrodinger.test.stu.common: Functions that are used in one or more modules.
    - schrodinger.test.stu.constants: Stores data that is used in one or more script.
    - schrodinger.test.stu.outcomes: Module containing STU workups.
      - schrodinger.test.stu.outcomes.compareDesmondSystems: script used to compare two desmond systems
      - schrodinger.test.stu.outcomes.compare_csv: See compare_csv docstring
      - schrodinger.test.stu.outcomes.correlate_workup
      - schrodinger.test.stu.outcomes.custom: Workups that are specific to one (or maybe a couple) or tests should live in this directory.
        
        schrodinger.test.stu.outcomes.custom.demo_custom_workup
        
        schrodinger.test.stu.outcomes.custom.glide
        
        schrodinger.test.stu.outcomes.custom.jaguar: workups used only in Jaguar.
        
        schrodinger.test.stu.outcomes.custom.perceptual_diff: Contains the workup is perceptual_diff
      - schrodinger.test.stu.outcomes.desmond_workups: Desmond workup techniques, all based on actual numerical results.
      - schrodinger.test.stu.outcomes.failures: STU workup exception types.
      - schrodinger.test.stu.outcomes.jaguar: Provides the jaguarDiff workup method for use with jaguar and qsite jobs.
      - schrodinger.test.stu.outcomes.job_status: Contains workups relating to the exit status of the job.
      - schrodinger.test.stu.outcomes.prime_workups
      - schrodinger.test.stu.outcomes.smarts_check
      - schrodinger.test.stu.outcomes.standard_workups: Contains the class _PropertyCompare, and several functions to perform test workups.
      - schrodinger.test.stu.outcomes.structure_comparisons: Provides functions for comparing structure files.
    - schrodinger.test.stu.process_management: Manage processes started by STU.
    - schrodinger.test.stu.run: Contains TestJCJob, TestSPJob, TestQueue, and Runner classes.
    - schrodinger.test.stu.sysinfo: Access to system information on machine, which could be Linux, Mac or Windows, and could be local or remote.
    - schrodinger.test.stu.testscripts: Contains the class TestScript, which provides methods to create, modify, extract and delete a test script.
    - schrodinger.test.stu.workup: Runs workups.
  - schrodinger.test.test_BondRotator
  - schrodinger.test.test_markers: Container for test marker functions.
- schrodinger.trajectory: Modules for prody-related analysis
  - schrodinger.trajectory.BondRotator
  - schrodinger.trajectory.Torsion
  - schrodinger.trajectory.analysis: A module of classes to analyze Desmond trajectories.
  - schrodinger.trajectory.analysistool: Contains a base class AnalysisTool for creating analyses of schrodinger.trajectory.desmondsimulation.DesmondSimulation objects.
  - schrodinger.trajectory.analyze_trajectories
  - schrodinger.trajectory.atomselection: A group of classes to help select atoms from trajectory frames.
  - schrodinger.trajectory.automatic_analysis_generator
  - schrodinger.trajectory.cmsstructure: A core class (CmsStructure) that is a complete description of the Desmond model system.
  - schrodinger.trajectory.desmondsimulation: A module to provide access to a Desmond simulation.
  - schrodinger.trajectory.ffstructure: A wrapper module to ease use of the mmffio library.
  - schrodinger.trajectory.hydrophobiccontactfinder: A module of classes to analyze Desmond trajectories.
  - schrodinger.trajectory.jcoupling: A module of classes to analyze NMR Jcouplings in Desmond trajectories.
  - schrodinger.trajectory.lipid_analysis: A modue of classes to analyze Desmont trajectories of bilayer systems
  - schrodinger.trajectory.pbc_manager
  - schrodinger.trajectory.prody: Modules for trajectory analysis and manipulation.
    - schrodinger.trajectory.prody.compare: This module defines functions for comparing normal modes from different models.
    - schrodinger.trajectory.prody.ensemble
    - schrodinger.trajectory.prody.main
    - schrodinger.trajectory.prody.main2
    - schrodinger.trajectory.prody.mode: This module defines classes for handling mode data.
    - schrodinger.trajectory.prody.modeset: This module defines a pointer class for handling subsets of normal modes.
    - schrodinger.trajectory.prody.nma: This module defines a class handling normal mode analysis data.
    - schrodinger.trajectory.prody.pca: This module defines classes for principal component analysis (PCA) and essential dynamics analysis (EDA) calculations.
    - schrodinger.trajectory.prody.test_arrow
    - schrodinger.trajectory.prody.writenmd: This module defines input and output functions for NMD format.
  - schrodinger.trajectory.protliginteractionfinder: Developed by Dmitry Lupyan
  - schrodinger.trajectory.rdf
  - schrodinger.trajectory.rdf_backend
  - schrodinger.trajectory.rmsd2d: A module to calculte 2D RMSD for Desmond trajectories using threading/multiprocessing.
  - schrodinger.trajectory.saltbridgefinder: A module of classes to analyze Desmond trajectories.
- schrodinger.ui: A package for Schrodinger user interface modules.
  - schrodinger.ui.appframework: GUI classes that mimic Maestro panels and dialogs.
  - schrodinger.ui.chooseligand
  - schrodinger.ui.dendro
  - schrodinger.ui.ligfilter: Components for creating GUIs that set up Ligfilter jobs.
  - schrodinger.ui.ligfilter_definition_dialog_ui
  - schrodinger.ui.ligfilter_ui
  - schrodinger.ui.macromodel: MacroModel GUI components with Maestro look and feel that are designed to plug and play with the schrodinger.ui.appframework.AppFramework class.
  - schrodinger.ui.maestroui
  - schrodinger.ui.multilistbox: Table-like multiple item list box class.
  - schrodinger.ui.picking
  - schrodinger.ui.propertyselector
  - schrodinger.ui.qt
    - schrodinger.ui.qt.appframework
    - schrodinger.ui.qt.pop_up_widgets
    - schrodinger.ui.qt.appframework2
      - schrodinger.ui.qt.appframework2.settings
      - schrodinger.ui.qt.appframework2.af2
      - schrodinger.ui.qt.appframework2.maestro_callback
      - schrodinger.ui.qt.appframework2.markers
      - schrodinger.ui.qt.appframework2.validation
    - schrodinger.ui.qt.structure2d
    - schrodinger.ui.qt.filedialog
    - schrodinger.ui.qt.rama
    - schrodinger.ui.qt.smatplotlib
    - schrodinger.ui.qt.navtoolbar
    - schrodinger.ui.qt.swidgets
    - schrodinger.ui.qt.utils
    - schrodinger.ui.qt.propertyselector
    - schrodinger.ui.qt.table_helper
    - schrodinger.ui.qt.structtable
    - schrodinger.ui.qt.table
  - schrodinger.ui.rama
  - schrodinger.ui.residueselector
  - schrodinger.ui.sequencealignment
    - schrodinger.ui.sequencealignment.globals
    - schrodinger.ui.sequencealignment.constants
    - schrodinger.ui.sequencealignment.sequence_viewer
  - schrodinger.ui.sketcher
  - schrodinger.ui.widget: Schrodinger-specific Tk widgets, including PMW widgets.
    - schrodinger.ui.widget._private
    - schrodinger.ui.widget.default: Functions to set up defaults so that Tkinter widgets match the old Schrodinger GUI style.
    - schrodinger.ui.widget.pmwwidget: This module contains all Schrodinger-specific PMW widgets.
    - schrodinger.ui.widget.tkinterwidget: Schrodinger themed Tkinter widgets.
  - schrodinger.ui.widgettable: A table whose cells contain Tkinter widgets such as Buttons and Checkbuttons.
- schrodinger.utils: Schrodinger utility modules.
  - schrodinger.utils._colorscheme
  - schrodinger.utils.cmdline: Functions and classes to assist in standard processing of command line arguments.
  - schrodinger.utils.colorscheme
  - schrodinger.utils.config: A module for getting software configuration(web center urls for now)
  - schrodinger.utils.csv_unicode: A wrapper around Python's csv module that allows it to work with Unicode characters.
  - schrodinger.utils.documentation
  - schrodinger.utils.env
  - schrodinger.utils.fileutils: A module of file utilities to deal with common file issues.
  - schrodinger.utils.imputils: Importing utilities.
  - schrodinger.utils.license: Contains a class License that allows easy licensing of Python scripts
  - schrodinger.utils.licutils: Licence related helper functions.
  - schrodinger.utils.ligfilter: Support module for Ligfilter applications, including parsing functions, filtering criteria, constants, and setting up of the default composite SMARTS patterns.
  - schrodinger.utils.log: Schrodinger logging utilities, including configuration.
  - schrodinger.utils.mmutil
  - schrodinger.utils.moduleproxy: A module proxy class to be used when a non-essential module can't be imported.
  - schrodinger.utils.preferences: A module to make the interface to the mmpref library more Pythonic.
  - schrodinger.utils.pymol: Utilities to load Maestro projects into PyMOL.
  - schrodinger.utils.sea: Functionality for "ark" file format handling.
  - schrodinger.utils.sshconfig: The sshconfig module contains code to configure Passwordless SSH.
  - schrodinger.utils.subproc: A wrapper to the standard library subprocess module.
  - schrodinger.utils.subprocess: A wrapper to the standard library subprocess module.
  - schrodinger.utils.sysinfo: Gather information about current system.
  - schrodinger.utils.timers: Timer classes.
  - schrodinger.utils.unicodesupport: Functions for encoding/decoding strings in files and paths
  - schrodinger.utils.urllib