Package schrodinger

This is the top level package for all Schrodinger modules.

The main modules of interest are schrodinger.structure and the ones in the schrodinger.structutils package.

The Python Module Overview included with the Schrodinger distribution gives an expository introduction to the Schrodinger Python API. It is available from the Help -> Python Module Overview... link in Maestro, or from the $SCHRODINGER/docs/python_api/overview.html file.

If you have questions about the API, please contact us at help@schrodinger.com.

Version: 57009

Submodules

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schrodinger.Qt: "A compatibility layer that lets us access PyQt without worrying about what version is available.
- schrodinger.Qt.PyQt5
- schrodinger.Qt.QtCore
- schrodinger.Qt.QtGui
- schrodinger.Qt.QtNetwork
- schrodinger.Qt.QtOpenGL
- schrodinger.Qt.QtPrintSupport
- schrodinger.Qt.QtSvg
- schrodinger.Qt.QtTest
- schrodinger.Qt.QtWebKit
- schrodinger.Qt.QtWebKitWidgets
- schrodinger.Qt.QtWidgets
schrodinger.analysis: A package for analysis modules.
- schrodinger.analysis.cluster: Provides a class for clustering a set of values - for example, 3D coordinates.
- 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.reaction: A module to support chemical reactions, retrosynthetic analysis, and reaction enumeration.
- schrodinger.analysis.transformations: Module to support chemical transformations defined via reaction SMARTS (RDKit dialect).
- 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.actions.icons_rc
  - 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.escomp: Module for using APBS to find electrostic potential on the protein surface to analyze protein-protein (or protein-ligand) interactions.
  - schrodinger.application.bioluminate.interaction_calculator: This module defines the InteractionCalculator class, which can be used for finding interactions between two groups of atoms.
  - schrodinger.application.bioluminate.patch_utils
    - schrodinger.application.bioluminate.patch_utils.patch_finder
    - schrodinger.application.bioluminate.patch_utils.pre_analyze: Run pre-analysis on the specified structure.
    - schrodinger.application.bioluminate.patch_utils.settings: Classes for storing panel settings.
  - 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_protein_docking_shared
  - schrodinger.application.bioluminate.protein_report_widget: Analyzes the quality of the structure in the workspace in terms of bond length, bond angles, dihedral values, peptide geometry, and other quantities.
  - schrodinger.application.bioluminate.protein_structure_quality: View the Ramachandran plot and Protein Report in a way that is interactive with the workspace.
  - schrodinger.application.bioluminate.protein_structure_quality_ui
  - schrodinger.application.bioluminate.reactive_residues: Identify protein sequences that are likely:
  - 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: A module containing a class for labeling atoms in the workspace.
- 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: Canvas clustering functionality that uses GUI libraries
  - 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: Higher-level wrappers to the Canvas Fingerprint generation and manipulation classes with GUI components.
  - schrodinger.application.canvas.r_group: r_group.py
  - 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: Support for Canvas fingerprint similarity operations that use GUI components.
  - schrodinger.application.canvas.topo_descriptors: Module which computes constitutional and topological descriptors, walk and path counts, and connectivity indices.
  - 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.bennett
  - schrodinger.application.desmond.bld_def
  - schrodinger.application.desmond.bld_ver
  - 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: This file contains common utility methods and classes used in several FEP scripts.
  - 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: The central interface for reading and editing Maestro format chemical sructures with force field data.
  - schrodinger.application.desmond.frag_snap
  - schrodinger.application.desmond.framesettools
  - 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.generictrajectory: The generic trajectory module provides an interface to the unified trajectory reader object.
  - schrodinger.application.desmond.gui: GUI code for the Desmond panels.
  - 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: Description: A module to generate average structure from watermap trajectory.
    - schrodinger.application.desmond.mdpose.mdpose_glide
    - schrodinger.application.desmond.mdpose.mdpose_neutralize
    - schrodinger.application.desmond.mdpose.mdpose_strain_energy
    - schrodinger.application.desmond.mdpose.mdposejob: Description: A module to handle running different MD Application related jobs.
  - 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: Multisim startup script.
  - schrodinger.application.desmond.packages
    - schrodinger.application.desmond.packages.analysis: Classes and functions for trajectory-based analysis
    - schrodinger.application.desmond.packages.cui: Common command-line interface for Desmond scripts
    - schrodinger.application.desmond.packages.enhanced_sampling
    - schrodinger.application.desmond.packages.gdesmond_utils
    - schrodinger.application.desmond.packages.msys: This is the high-level Python interface for msys, intended for use by chemists.
      - schrodinger.application.desmond.packages.msys._cealign
      - schrodinger.application.desmond.packages.msys._msys
      - schrodinger.application.desmond.packages.msys.atomsel
      - schrodinger.application.desmond.packages.msys.cealign
      - schrodinger.application.desmond.packages.msys.grease
      - schrodinger.application.desmond.packages.msys.groups
      - schrodinger.application.desmond.packages.msys.knot: Given a system, find any instances where a bond is 'threaded' through a ring, like so
      - schrodinger.application.desmond.packages.msys.molfile: Structure and coordinate file manipulation library.
        
        schrodinger.application.desmond.packages.msys.molfile._molfile
        
        schrodinger.application.desmond.packages.msys.molfile.findframe
      - schrodinger.application.desmond.packages.msys.pfx: A high level interface for wrapping, centering, and alignment.
      - schrodinger.application.desmond.packages.msys.posre
      - schrodinger.application.desmond.packages.msys.reorder
      - schrodinger.application.desmond.packages.msys.sequence
      - schrodinger.application.desmond.packages.msys.thermalize
      - schrodinger.application.desmond.packages.msys.update
      - schrodinger.application.desmond.packages.msys.validate
      - schrodinger.application.desmond.packages.msys.vdw
      - schrodinger.application.desmond.packages.msys.wrap
    - schrodinger.application.desmond.packages.timer: Facilities for timing a block of code.
    - schrodinger.application.desmond.packages.topo: Functionalities to handle molecular topologies
    - schrodinger.application.desmond.packages.traj: Molecular dynamics trajectory handling module Define common APIs for various trajectory formats.
    - schrodinger.application.desmond.packages.traj_util: Advanced utilities for trajectory handling
    - schrodinger.application.desmond.packages.united
    - schrodinger.application.desmond.packages.viparr
    - schrodinger.application.desmond.packages.viparr1
  - schrodinger.application.desmond.periodicfix
  - schrodinger.application.desmond.picklejar: Facilities for pickling objects that are otherwise uneasy to pickle, e.g., class attributes.
  - schrodinger.application.desmond.platforms: Non-gui code related to Desmond's unavailability on some platforms.
  - 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: Collection of modules to repair structures to be used for desmond simulation
  - 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: It prepares or runs a REST MD job.
  - 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: FEP+ generator Version 0.1
    - 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: FEP+ command line UI Version 0.1
      - schrodinger.application.desmond.starter.ui.multisim: Multisim command line UI
  - 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: The script truncates protein beyond truncate_distance from ligand atoms, restrain remaining protein heavy atoms beyond restrain_distance from ligand atoms, and solvate it by solvent_buffer distance.
  - 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
- 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: Classes for creating Grid Generation and Ligand Docking DICE (Impact) input files from user-friendly keyword/value pairs.
  - schrodinger.application.glide.glideanalysis: Functions and classes for calculating Glide Docking Enrichment Factors and creating sorted pose libraries.
  - schrodinger.application.glide.gui: Classes and functions that are shared between the Glide GridGen and Docking panels.
  - schrodinger.application.glide.http_client: Glide HTTP client
  - schrodinger.application.glide.http_server: Glide HTTP Server
  - schrodinger.application.glide.packages
    - schrodinger.application.glide.packages.driver: This module contains classes and functions needed by the Glide driver.
    - schrodinger.application.glide.packages.ensemble_optimizer
    - schrodinger.application.glide.packages.glide_subset
    - schrodinger.application.glide.packages.startup: Classes and functions used by the Glide startup script.
    - schrodinger.application.glide.packages.testing
    - schrodinger.application.glide.packages.utils
  - 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 blocks from pose files.
- schrodinger.application.inputconfig: A modified version of the configobj module.
- schrodinger.application.jaguar: Jaguar-related modules.
  - schrodinger.application.jaguar.autots_bonding: Methods to handle structure reading and bonding in AutoTS.
  - schrodinger.application.jaguar.autots_constants
  - schrodinger.application.jaguar.autots_exceptions: Custom AutoTS exceptions
  - schrodinger.application.jaguar.autots_rmsd: methods for comparison of structures using rmsd
  - schrodinger.application.jaguar.basis: Utility functions for dealing with Jaguar basis sets
  - schrodinger.application.jaguar.check_headers
  - schrodinger.application.jaguar.chirality
  - schrodinger.application.jaguar.constants: Constants used in unit conversion.
  - schrodinger.application.jaguar.exceptions: Some custom Jaguar exception classes
  - schrodinger.application.jaguar.file_logger: General classes and functions related to output files, in particular when running under jobcontrol.
  - schrodinger.application.jaguar.global_macros
  - schrodinger.application.jaguar.gui
    - schrodinger.application.jaguar.gui.base_panel
    - schrodinger.application.jaguar.gui.basis_selector
    - schrodinger.application.jaguar.gui.edit_dialog
    - schrodinger.application.jaguar.gui.filedialog: Custom file dialogs for the Jaguar GUIs
    - schrodinger.application.jaguar.gui.input_tab_widgets
    - schrodinger.application.jaguar.gui.input_tab_widgets_hb
    - schrodinger.application.jaguar.gui.input_tab_widgets_pka
    - schrodinger.application.jaguar.gui.tabs
    - schrodinger.application.jaguar.gui.theory_tab_widgets
    - schrodinger.application.jaguar.gui.ui
    - schrodinger.application.jaguar.gui.utils: Utility functions and classes for the Jaguar GUIs
  - schrodinger.application.jaguar.input: Functions and classes for reading and creating Jaguar input files.
  - schrodinger.application.jaguar.jaguar_diff: Classes for parsing Jaguar output files and accessing output properties programmatically.
  - schrodinger.application.jaguar.jaguar_keyword_utils: functions to help grab keywords from xml and jaguar input files
  - schrodinger.application.jaguar.keywordDB
  - schrodinger.application.jaguar.make_headers
  - 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.reactiq_input: Functions and classes for defining the input to a Reactiq workflow.
  - schrodinger.application.jaguar.reactiq_input_constants: Constants used by ReactiqInput
  - schrodinger.application.jaguar.reactiq_keywords: This module documents all possible Reactiq input keywords.
  - schrodinger.application.jaguar.reactiq_validation: Reactiq keywords input validation and specialized Exceptions
  - schrodinger.application.jaguar.results: 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.textparser: Classes for parsing Jaguar output files and accessing output properties programmatically.
  - schrodinger.application.jaguar.user_config: User profiles and configuration support for Jaguar input files
  - schrodinger.application.jaguar.utils: Jaguar utility functions.
  - schrodinger.application.jaguar.validation: Jaguar keywords input validation and custom Exceptions
- schrodinger.application.licensing: Licensing-related modules.
  - schrodinger.application.licensing.flexlm
  - schrodinger.application.licensing.licadmin
  - schrodinger.application.licensing.licerror
  - schrodinger.application.licensing.lmgrd_log_parser
  - schrodinger.application.licensing.netsuiteapi
- schrodinger.application.ligprep: LigPrep related modules.
  - schrodinger.application.ligprep.ionizer: Ionizer module.
- 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: Copyright Schrodinger, LLC.
  - 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: Builder classes for making amorphous cells
  - schrodinger.application.matsci.atomicsymbols: The full set of atomic symbols and characters that begin atomic symbols.
  - schrodinger.application.matsci.atomicsymbolsgui: GUI elements that help with atomic symbols
  - schrodinger.application.matsci.bandshape_utils
  - schrodinger.application.matsci.basiselements: Copyright Schrodinger, LLC.
  - schrodinger.application.matsci.buildcomplex: This module assists in building organometallic complexes.
  - schrodinger.application.matsci.builderwidgets: Common widgets and code for builders such as the TM Complex Builder and the Oligamer builder
  - schrodinger.application.matsci.cgforcefield: Constants, functions and classes for assigning coarse-grained force fields to structures
  - schrodinger.application.matsci.cgforcefieldgui: GUI items for use with coarse grain force fields
  - schrodinger.application.matsci.chargegui: Classes to aid in assigning charges to atoms in a GUI
  - schrodinger.application.matsci.clusterstruct: Functions to aid in pulling dimers or clusters of nearest neighbors from a larger structure.
  - schrodinger.application.matsci.clusterstructgui: GUI elements to aid in pulling dimers or clusters of nearest neighbors from a larger structure.
  - schrodinger.application.matsci.coarsegrain: Utilities for working with coarse grain structures
  - schrodinger.application.matsci.controlicons_rc
  - schrodinger.application.matsci.desmondutils: Utilities for working with Desmond.
  - schrodinger.application.matsci.enumeration: A class and function that help enumerate possibilities - could be enumerating over items of a list or enumerating the element at various atom positions in a structure, for instance.
  - schrodinger.application.matsci.equilibrium_md: Equilibrium molecular dynamics classes/function shared by transport property calculations using Einstein and Green-Kubo methods.
  - schrodinger.application.matsci.espresso: Quantum Espresso integration functionality
    - schrodinger.application.matsci.espresso.ppdb: Classes and functions to deal with pseudopotentials database.
    - schrodinger.application.matsci.espresso.qeinput: Classes and functions to deal with XML input generation for Quantum Espresso.
    - schrodinger.application.matsci.espresso.qeoutput: Classes and functions to deal reading XML generated by Quantum Espresso.
    - schrodinger.application.matsci.espresso.utils: Copyright Schrodinger, LLC.
  - schrodinger.application.matsci.genetic_optimization: Genetic optimization module.
    - schrodinger.application.matsci.genetic_optimization.genetic_optimization: Classes and functions for the genetic optimization module.
  - schrodinger.application.matsci.guibase: GUI classes/function shared by multiple Materials Science panels.
  - schrodinger.application.matsci.jaguarworkflows: Workflow and Step classes to aid in running a series of Jaguar jobs.
  - schrodinger.application.matsci.jobdirdlg: A dialog for obtaining a job directory of a previously submitted job
  - schrodinger.application.matsci.jobutils: Copyright Schrodinger, LLC.
  - schrodinger.application.matsci.mecp_mod: Classes and functions for finding MECPs.
  - schrodinger.application.matsci.montecarlo: Classes related to Monte Carlo simulations
  - schrodinger.application.matsci.msutils: Utility functions and classes for MatSci workflows.
  - schrodinger.application.matsci.mswidgets: Contains widgets that are useful in MatSci panels.
  - schrodinger.application.matsci.nano: Nanostructure module.
    - schrodinger.application.matsci.nano.check: Classes and functions for checking nanostructure input.
    - schrodinger.application.matsci.nano.constants: Constants for building nanostructures.
    - schrodinger.application.matsci.nano.interface_mod: Classes and functions to create interface models.
    - schrodinger.application.matsci.nano.particle: Classes and functions to create nanoparticles.
    - schrodinger.application.matsci.nano.plane: Classes and functions for crystal planes.
    - schrodinger.application.matsci.nano.sheet: Classes and functions for making honeycomb nanosheets.
    - schrodinger.application.matsci.nano.slab: Classes and functions to create surface models.
    - schrodinger.application.matsci.nano.surfaces_interfaces_mod: Classes and functions to enumerate surfaces and interfaces.
    - schrodinger.application.matsci.nano.tube: Classes and functions for building single- and multi-walled nanotubes.
    - schrodinger.application.matsci.nano.util: Utility functions for nanostructures.
    - schrodinger.application.matsci.nano.xtal: Classes and functions for creating crystals by unit cell.
  - schrodinger.application.matsci.optoelectronics: Constants and other commonly used optoelectronics objects
  - schrodinger.application.matsci.parserutils: Utilities for working with argument parsers
  - 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: Classes and functions for building reaction channels.
  - schrodinger.application.matsci.rxn_path: Classes and functions for generating reaction paths.
  - schrodinger.application.matsci.shapes: Classes and functions to handle various shapes.
  - schrodinger.application.matsci.smartsutils
  - schrodinger.application.matsci.smartsutilsgui
  - schrodinger.application.matsci.spectra: Copyright Schrodinger, LLC.
  - schrodinger.application.matsci.textlogger: Class to set up a nicely formatted logger
  - schrodinger.application.matsci.zmutils: Contains classes for working with Z-Matrices
- 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: Classes for dealing with graphs for constructing optimal FEP pathways.
  - schrodinger.application.mcpro.read_output: Class to read summary/monitor file.
  - schrodinger.application.mcpro.residuetools: Classes for manipulating residues.
  - schrodinger.application.mcpro.solvent
  - schrodinger.application.mcpro.writeinputs: Classes for writing input.
  - schrodinger.application.mcpro.zmat: Z-matrix classes and functions.
- schrodinger.application.medchem
  - schrodinger.application.medchem.property: Functions for computing medchem properties.
- schrodinger.application.mopac: MOPAC-related modules.
  - schrodinger.application.mopac.exceptions: Some custom MOPAC exception classes
  - schrodinger.application.mopac.mopac_backend: Driver script for running MOPAC7.1 and MOPAC2012 backend execs.
  - schrodinger.application.mopac.mopac_launchers: This module contains classes for launching different MOPAC versions.
  - schrodinger.application.mopac.mopac_parser: Command line parsing for the MOPAC backend.
  - schrodinger.application.mopac.mopac_results: This is for parsing output from different MOPAC versions.
  - schrodinger.application.mopac.mopac_startup: Startup driver for running semiempirical calculations (i.e.
  - 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.command
  - schrodinger.application.msv.domain
    - schrodinger.application.msv.domain.align
    - schrodinger.application.msv.domain.alignment: Classes for working with sequences containing alignment information (gaps) and collections thereof.
    - schrodinger.application.msv.domain.annotation: Implementation of Multiple Sequence Viewer Annotation class.
    - schrodinger.application.msv.domain.constants
    - schrodinger.application.msv.domain.residue
    - schrodinger.application.msv.domain.sequence: Implementation of multiple sequence viewer Sequence class.
  - schrodinger.application.msv.gui
    - schrodinger.application.msv.gui.color: Contains the color scheme constants for msv
    - schrodinger.application.msv.gui.color_editor
    - schrodinger.application.msv.gui.color_editor_ui
    - schrodinger.application.msv.gui.delegates: Qt Delegates for the tree view.
    - schrodinger.application.msv.gui.dendrogram_viewer
    - schrodinger.application.msv.gui.get_sequences_dialog
    - schrodinger.application.msv.gui.get_sequences_dialog_ui
    - schrodinger.application.msv.gui.menu
    - schrodinger.application.msv.gui.msv_gui
    - schrodinger.application.msv.gui.msv_main_ui
    - schrodinger.application.msv.gui.msv_main_window_ui
    - schrodinger.application.msv.gui.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.msv.gui.msv_rc
    - schrodinger.application.msv.gui.msv_widget
    - schrodinger.application.msv.gui.popup_dialogs
    - schrodinger.application.msv.gui.rename_tab_dialog_ui
    - schrodinger.application.msv.gui.stylesheets
    - schrodinger.application.msv.gui.tab_widget
    - schrodinger.application.msv.gui.undoable_alignment
    - schrodinger.application.msv.gui.view
    - schrodinger.application.msv.gui.viewconstants: Constants that are shared between the view and viewmodel modules.
    - schrodinger.application.msv.gui.viewmodel
  - schrodinger.application.msv.io
    - schrodinger.application.msv.io.converters: Utilities for converting between different sequence and sequence group objects.
    - schrodinger.application.msv.io.seqio
    - schrodinger.application.msv.io.structure_model
  - schrodinger.application.msv.jobs
  - 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.msv.utils
- schrodinger.application.phase: Phase-related modules.
  - schrodinger.application.phase.constants: Module defining Phase-related constants that are shared between scripts and other modules.
  - schrodinger.application.phase.create_xvol: Phase driver for the Develop Common Pharmacophore Hypotheses (DHCP) workflow.
  - schrodinger.application.phase.featureselector: Widget for letting the user show/hide or enable/disable features in a hypothesis.
  - schrodinger.application.phase.hypothesis: Module for reading and writing Phase hypotheses.
  - schrodinger.application.phase.hypothesis_binding_modes: Clusters actives and hypotheses into possible binding modes.
  - schrodinger.application.phase.input: Module for reading and writing Phase configuration/input files.
  - schrodinger.application.phase.packages
    - schrodinger.application.phase.packages.phase_convert_MOE: Module for converting MOE *.ph4 hypotheses into Schrodinger Phase *.phypo format.
  - schrodinger.application.phase.phase_markers: Phase pharmacophore workspace markers.
  - schrodinger.application.phase.phase_widgets
- schrodinger.application.pldb
  - schrodinger.application.pldb.packages
    - schrodinger.application.pldb.packages.pldb_file_upload_shell: $Revision: PLACEHOLDER$
    - schrodinger.application.pldb.packages.pldb_gui_shell: $Revision: PLACEHOLDER$
    - schrodinger.application.pldb.packages.pldb_gui_shell_dir
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.base_branding_config_shell: Shell copy of pldb_gui_dir.base_branding_config
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.branding_config_chemdb_shell: Shell copy of pldb_gui_dir.branding_config_chemdb
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.branding_config_materials_shell: Shell copy of pldb_gui_dir.branding_config_materials
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.branding_config_shell
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.client_shell: Shell REST client for accessing PLDB server.
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.controller_shell
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.credentials_dialog_shell: A shell dialog for user credentials.
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.logger_shell: Shell copy of pldb_gui_dir.logger
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.ui
        
        schrodinger.application.pldb.packages.pldb_gui_shell_dir.ui.credentials_dialog_ui
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.utils_shell: Shell version of pldb_gui_dir.utils
      - schrodinger.application.pldb.packages.pldb_gui_shell_dir.version_shell: Shell copy of pldb_gui_dir.version
- 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: This is a class that generates watermap input files and runs them through jobcontrol.
  - 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.graphics3d.torus: OpenGL toruses.
schrodinger.infra: Infrastructure modules, including wrappers to basic mmlib types.
- 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 Python exception handler that prevents uncaught exceptions in Python scripts from crashing Maestro.
- schrodinger.infra.exception_handler_dir
  - schrodinger.infra.exception_handler_dir.exception_dialog
  - schrodinger.infra.exception_handler_dir.exception_dialog_ui
- schrodinger.infra.fast3d: Fast3D wrappers
- 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.mmjob
- 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: This module 'mopac' is auto-generated with f2py (version:2).
- 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.pyqt4_compat
- 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.jobapi
- schrodinger.job.jobcontrol: Core job control for python.
- schrodinger.job.jserver_client
- schrodinger.job.launchapi: Provide an API that allows a definition of a job.
- schrodinger.job.launcher: A class for launching individual executables under job control.
- schrodinger.job.launchparams
- 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.commands
- schrodinger.maestro.maestro: Core functions for interaction with Maestro.
- schrodinger.maestro.markers: Module for placing markers in the Workspace.
schrodinger.mpl_backend: A PyQt upgrade compatibility module that acts as backend_qt4 in PyQt4 builds and backend_qt5 in PyQt5 builds.
schrodinger.mpl_backend_agg: A PyQt upgrade compatibility module that acts as backend_qt4agg in PyQt4 builds and backend_qt5agg in PyQt5 builds.
schrodinger.pipeline: Modules for the Pipeline mechanism used by VSW & QPLD.
- schrodinger.pipeline.compiled_functions: Code for pipeline that should only be distibuted in compiled form.
- schrodinger.pipeline.input: Classes for writing Pipeline input files.
- schrodinger.pipeline.pipeio: Core Pipeline I/O classes (Structures, Grid, and Text, and PhaseDB).
- schrodinger.pipeline.pipeline: Classes for running pipelines.
- schrodinger.pipeline.pipeutils: Shared functions for Pipeline stages.
- schrodinger.pipeline.stage: Base classes for Pipeline stages.
- schrodinger.pipeline.stages: Pipeline stage modules used by VSW and QPLD.
  - schrodinger.pipeline.stages.canvas: This module contains stages for running Canvas calculations.
  - schrodinger.pipeline.stages.combine: Core stages for Pipeline mechanism.
  - schrodinger.pipeline.stages.convert: Stage for converting structure files from one format to another.
  - schrodinger.pipeline.stages.example
  - schrodinger.pipeline.stages.filtering: Stages related to filtering structures.
  - schrodinger.pipeline.stages.gencodes: Stage for generating and storing codes for ligands/compounds and variants.
  - schrodinger.pipeline.stages.glide: Glide Docking & Gridgen stages.
  - schrodinger.pipeline.stages.ligprep: Stages for running LigPrep.
  - schrodinger.pipeline.stages.macromodel: Stages for running MacroModel jobs.
  - schrodinger.pipeline.stages.phase: Stages for running Phase jobs.
  - schrodinger.pipeline.stages.prime: A stage for running Prime jobs.
  - schrodinger.pipeline.stages.pull: A stage for extracting a subset of ligands/compounds.
  - schrodinger.pipeline.stages.qikprop: A stage for running QikProp jobs.
  - schrodinger.pipeline.stages.qsite: A stage for running QSite jobs.
  - schrodinger.pipeline.stages.rmsd: A stage for calculating RMSDs for structures in two sets.
  - schrodinger.pipeline.stages.semiemp: Stage for running semi-empirical jobs.
schrodinger.project: A module for accessing and modifying a Maestro Project.
schrodinger.project_surface: Pythonic wrappings for mmsurf surfaces retrieved from a project
schrodinger.protein: Protein related modules, including functionality for analysis and manipulation.
- schrodinger.protein._reliability: This module is for assessing protein reliability and fitness for various structure-based applications.
- schrodinger.protein.analysis: A class for diagnosing and reporting common structural problems of protein complexes.
- schrodinger.protein.analysis_params
- schrodinger.protein.assignment: Module for optimizing hydroxyl, thiol and water orientiations, Chi-flips of asparagine, glutamine and histidine, and protonation states of aspartic acid, glutamic acid, and histidine.
- schrodinger.protein.captermini: Module for capping uncapped terminal residues in a protein structure by adding NME or ACE caps as appropriate.
- schrodinger.protein.findhets: Module for finding 'het' groups in a protein structure.
- schrodinger.protein.getpdb: Module for downloading PDB files from the web.
- schrodinger.protein.getpdb_utility: Copy a PDB file out of the PDB directory, or, if not found, download it from the rcsb repository: http://www.rcsb.org/pdb/files/.
- schrodinger.protein.helix: Module for converting residue sequences to 3D structures with an a-helix secondary structure.
- 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: A module containing the central interface for reading and editing chemical structures.
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.filter: Functions and classes for filtering structure files based on properties or SMARTS patterns.
- schrodinger.structutils.interactionfp: Calculate structural interaction fingerprints.
- schrodinger.structutils.interactions: A module for detecting interactions between structures.
  - schrodinger.structutils.interactions.hbond: Module for identifying hydrogen and halogen bond interactions.
  - schrodinger.structutils.interactions.pi: A module for detecting pi-pi and pi-cation interactions.
  - schrodinger.structutils.interactions.salt_bridge: Find salt-bridge interactions.
  - schrodinger.structutils.interactions.steric_clash
- schrodinger.structutils.io: This module is deprecated.
- 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.rgroup_enumerate: Module for R-group enumeration.
- schrodinger.structutils.ringspear: Functions and classes useful for finding ring spears.
- schrodinger.structutils.rmsd: Functionality for calculating conformer RMSDs.
- schrodinger.structutils.sitealign: Perform a pairwise superposition of multiple structures using the C-alpha atoms of selected residues.
- 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.tasks
- schrodinger.tasks.jobtasks
- schrodinger.tasks.mappers
- schrodinger.tasks.parameters
- schrodinger.tasks.runners
- schrodinger.tasks.tasks
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: Saves an image of the current workspace taken directly fro the Qt Widget framebuffer rendering.
- schrodinger.test.ioredirect
- schrodinger.test.perceptualdiff: Run Perceptual Diff tests in maestrolibs
- 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.project_mock: This module has classes that can be used to mock out project related functionality that cannot be accessed from outside of Maestro for unit tests.
- schrodinger.test.pytest_customizations: Local Schrodinger py.test customizations.
- schrodinger.test.squish: Functions to help with Squish test writing.
  - schrodinger.test.squish.canvas: Modules for use with Canvas Squish tests.
    - schrodinger.test.squish.canvas.exception_handling: Exception handling.
    - schrodinger.test.squish.canvas.utils
  - schrodinger.test.squish.general: Modules for general use in any Squish test.
    - schrodinger.test.squish.general.general: General constants and function overrides for use with Squish.
  - schrodinger.test.squish.maestro: Modules for use with Maestro Squish tests.
    - schrodinger.test.squish.maestro.exception_handling: Exception handling.
    - schrodinger.test.squish.maestro.job_monitor: A class for interaction with Job Control directly using Schrodinger API.
    - schrodinger.test.squish.maestro.menubar: Functions for dynamically interacting with menus and menu items.
    - schrodinger.test.squish.maestro.project_table: A class for interaction with the Project Table.
    - schrodinger.test.squish.maestro.python_shell: A class for interaction with the Python Shell in Maestro which provides access to the Schrodinger API.
    - schrodinger.test.squish.maestro.utils: Maestro utils.
- 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
    - schrodinger.test.stu.outcomes.compareDesmondSystems': script used to compare two desmond systems
    - schrodinger.test.stu.outcomes.compare_csv
    - schrodinger.test.stu.outcomes.compare_csv': See compare_csv docstring
    - schrodinger.test.stu.outcomes.correlate_to_reference_file
    - schrodinger.test.stu.outcomes.correlate_workup
    - 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.asl_count
      - 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.custom.phase_workups: Special STU workups for testing Phase.
      - schrodinger.test.stu.outcomes.custom.reactiq: Special workups for testing Reactiq.
    - 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.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.stu.workups
    - schrodinger.test.stu.workups.workup_tools
- schrodinger.test.test_markers: Container for test marker functions.
schrodinger.thirdparty
- schrodinger.thirdparty.rdkit_adapter: Conversions between Schrodinger structure objects (mmct) and RDKit mol objects.
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.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.order_parameters: A modue of classes for calculating order parameters
- 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.crosscorrelation: This module defines functions for calculating atomic properties from normal modes.
  - 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.proteininteractionsfinder: A module of classes to analyze Desmond trajectories.
- schrodinger.trajectory.protliginteractionfinder: Developed by Dmitry Lupyan
- 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.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.maestro_ui
- schrodinger.ui.multilistbox: Table-like multiple item list box class.
- schrodinger.ui.picking
- schrodinger.ui.picking_dir
- schrodinger.ui.propertyselector: A PropertySelector Frame class for viewing and selecting properties.
- schrodinger.ui.qt: A package for Schrodinger Qt interface modules.
  - schrodinger.ui.qt.appframework: This module provides GUI classes that mimic Maestro panels and dialogs.
  - schrodinger.ui.qt.filedialog: Schrodinger version of the QFileDialog class of the QtGui module.
  - schrodinger.ui.qt.layout: Contains helpers for creating layouts.
  - schrodinger.ui.qt.propertyselector: This module provides a PropertySelector GUI class for viewing and selecting properties.
  - schrodinger.ui.qt.structtable: This module provides classes that can be used to create Qt tables that show 2D structures in the cells.
  - schrodinger.ui.qt.style: Module to manage Schrodinger-wide Qt style sheet.
- schrodinger.ui.rama: A Ramachandran Plot widget, along with some tools for manipulating structures/points.
- schrodinger.ui.residueselector
- schrodinger.ui.sequencealignment: Multiple Sequence Viewer functionality
- 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.utils: Schrodinger utility modules.
- 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.installation_check
- 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.units: A module containing common unit constants and conversion routines.
- schrodinger.utils.urllib: Functions that help access web URLs through proxy servers.
- schrodinger.utils.welcome_dialog
- schrodinger.utils.welcome_dialog_dir
  - schrodinger.utils.welcome_dialog_dir.base_welcome

Classes

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MaestroNotAvailableError
Error class to indicate that Maestro is not available and there was an attempt to use it.

_DummyMaestroModule
Used to replace schrodinger.maestro.maestro when running outside of Maestro.

Functions

[hide private]

get_maestro()
Get either schrodinger.maestro.maestro or an object that allows scripts to avoid running maestro dependent-code, and print reasonable errors if that code is run outside of maestro.

get_mmshare_version()
Return the mmshare version as a 5 digit integer.

get_mpl_backend_name()
Get the matplotlib backend name to use with pyplot.

get_release_name()
Return release name.

get_scisol_version()
Return the scisol version number as a 5 digit int as in version.h

version_at_least(v)
Check that the Schrodinger python version is at least the value 'v'.

version_at_most(v)
Check that the Schrodinger python version does not exceed 'v'.

version_compatible(minimum, maximum)
Check that the version is between minimum and maximum values.

Variables

[hide private]

__package__ = 'schrodinger'

Function Details

[hide private]

get_maestro()

Get either schrodinger.maestro.maestro or an object that allows scripts to avoid running maestro dependent-code, and print reasonable errors if that code is run outside of maestro.

Returns:: schrodinger.maestro.maestro or _DummyMaestroModule

get_release_name()

Return release name.

Current use of the release name is to specify a release-specific subdirectory in the user application data directory.

version_at_least(v)

Check that the Schrodinger python version is at least the value 'v'. NOTE: Deprecated in favor of get_mmshare_version()

version_at_most(v)

Check that the Schrodinger python version does not exceed 'v'. NOTE: Deprecated in favor of get_mmshare_version()

version_compatible(minimum, maximum)

Check that the version is between minimum and maximum values. NOTE: Deprecated in favor of get_mmshare_version()

If the current Schrodinger python version is less than the minimum, an Exception will be raised. If the current version is greater than the maximum, a warning will be issued.