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: 50011

Submodules

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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

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_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__ = None
hash(x)

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_compatible(minimum, maximum)

Check that the version is between minimum and maximum values.

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.