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: 45016

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.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: 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.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.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.classification_scheme: A module to implement a particular type of classification scheme.
    - schrodinger.application.combiglide.packages.core_classifier: A module to provide a core classification for use with the the core_classifiction module.
  - 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.covalent_fep_prep: Objective: Given proteins with covalent congeneric R groups prep ligands for mapper
  - 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.extend_fep: Notes on this modules: If I submit a job to extend edge A this will prepare and run a "subjob" which carries out extending the lambda stage and then a "master" job which will generate a new <jobname>_out_pv.mae, <jobname>_out.pkl, and <jobname>_multisim.log.
  - schrodinger.application.desmond.extend_fep_backend
  - 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_protein_prep
  - schrodinger.application.desmond.fep_reporter
  - 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.ffiostructure: The central interface for reading and editing Maestro format chemical sructures with force field data.
  - 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.gui_v2: 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.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.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.periodicfix
  - 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: 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_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.stage: Various multisim concrete stage classes.
  - 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.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.liaison_lsbd: Liaison class from the lsbd driver.
  - schrodinger.application.glide.poseviewconvert: Functions for creating or converting pose viewer files.
  - 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.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.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.scan: Support functions and classes for Jaguar scans.
  - schrodinger.application.jaguar.utils: Jaguar utility functions.
- schrodinger.application.lid: A package containing Ligand Interaction modules.
  - schrodinger.application.lid.lid2d: A package containing Ligand Interaction modules.
  - schrodinger.application.lid.lid_savedialog_ui
  - schrodinger.application.lid.ligand_interaction_diagram: Copyright Schrodinger, LLC.
  - schrodinger.application.lid.ligand_interaction_diagram_gui
  - schrodinger.application.lid.ligand_interaction_diagram_rc
  - schrodinger.application.lid.ligand_interaction_diagram_test
  - schrodinger.application.lid.ligand_interaction_diagram_ui
- 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.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.basiselements
  - schrodinger.application.matsci.buildcomplex: This module assists in building organometallic complexes.
  - schrodinger.application.matsci.jaguarworkflows: Workflow and Step classes to aid in running a series of Jaguar jobs.
  - schrodinger.application.matsci.jobutils
  - 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.sheet: Classes and functions for making honeycomb nanosheets.
    - 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.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.spectra
  - schrodinger.application.matsci.textlogger: Class to set up a nicely formatted logger
- 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.moldescriptors
  - schrodinger.application.moldescriptors.backend: A backend Python script that computes molecular indices for each input structure in the input file.
  - schrodinger.application.moldescriptors.gui: A Python panel to show a UI for the following: a) Topological Descriptors b) MOPAC properties c) QikProp ADME properties
  - schrodinger.application.moldescriptors.impl: A Python script that computes molecular indices for each input structure in the input file.
  - schrodinger.application.moldescriptors.startup: A simple Python script that acts as startup script of molecular descriptor backend.
- schrodinger.application.mopac: Functions for running MOPAC calculations and parsing results.
- schrodinger.application.phase: Phase-related modules.
  - schrodinger.application.phase.hypothesis: Module for reading and writing Phase hypotheses.
- schrodinger.application.prepwizard: Shared functionality between PrepWizard GUI and command-line PrepWizard.
- schrodinger.application.prime: Modules for dealing with Prime.
  - 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.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.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._licensing
- schrodinger.infra._mmgpgpu
- 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.mmsurf: C++ wrapper for surface related functionality
- schrodinger.infra.mopac: This module 'mopac' is auto-generated with f2py (version:2).
- schrodinger.infra.propedit: Support functions for Structure property manipulation functions in the propeditor script.
- 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.hunt_cache: Speed up hunt with caching.
- schrodinger.job.jobcontrol: Core job control for python.
- schrodinger.job.launcher: A class for launching individual executables under job control.
- schrodinger.job.queue: A class for running multiple jobs under job control.
- 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: 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.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 managing Phase databases.
  - 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.protein: Protein related modules, including functionality for analysis and manipulation.
- 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.remediate: A function for remediating PDB structures.
- 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.interactionfp: Calculate structural interaction fingerprints.
- schrodinger.structutils.interactions: A module for detecting interactions between structures.
  - 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: Classes and functions for reading and writing structure files.
- 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.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.test
- schrodinger.test.build_test_structures: Some convenience functions to quickly and reproducibly create structures for testing.
- 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.decorate_fflag: Enable or disable a feature flag in a specific situation.
- schrodinger.test.ioredirect
- schrodinger.test.performance: 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
    - 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_workup
    - schrodinger.test.stu.outcomes.correlate_workup'
    - schrodinger.test.stu.outcomes.desmond: This is a module for use in the backend test utility's workup routine.
    - 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.jaguarDiff
    - schrodinger.test.stu.outcomes.jaguarDiff': 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.outcomes.workup_desmond
    - schrodinger.test.stu.outcomes.workup_desmond': A module to run workup on Desmond's system builder jobs based on a cfg file.
  - 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_markers: Container for test marker functions.
schrodinger.trajectory: Modules for trajectory analysis and manipulation.
- 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: analyze_trajectories.py -- analyze a set of Desmond 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.pbc_manager
- schrodinger.trajectory.protliginteractionfinder: Developed by Dmitry Lupyan
- schrodinger.trajectory.rdf: This script will launch a Radial Distribution Function (RDF or g(r) or gofr) calculation.
- 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.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.multilistbox: Table-like multiple item list box class.
- schrodinger.ui.picking
- schrodinger.ui.propertyselector: A PropertySelector Frame class for viewing and selecting properties.
- schrodinger.ui.qt
  - schrodinger.ui.qt.appframework
  - schrodinger.ui.qt.swidgets
  - schrodinger.ui.qt.appframework2
    - schrodinger.ui.qt.appframework2.af2
    - schrodinger.ui.qt.appframework2.markers
    - schrodinger.ui.qt.appframework2.validation
  - schrodinger.ui.qt.filedialog
  - schrodinger.ui.qt.utils
  - schrodinger.ui.qt.structtable
  - schrodinger.ui.qt.table
  - schrodinger.ui.qt.structure2d
  - schrodinger.ui.qt.rama
  - schrodinger.ui.qt.smatplotlib
  - schrodinger.ui.qt.navtoolbar
  - schrodinger.ui.qt.propertyselector
- schrodinger.ui.rama: A Ramachandran Plot widget, along with some tools for manipulating structures/points.
- schrodinger.ui.sequencealignment
  - schrodinger.ui.sequencealignment.globals
  - schrodinger.ui.sequencealignment.sequence_viewer
  - schrodinger.ui.sequencealignment.maestro
  - schrodinger.ui.sequencealignment.fileio
  - schrodinger.ui.sequencealignment.jobs
  - schrodinger.ui.sequencealignment.sequence_group
  - schrodinger.ui.sequencealignment.align
  - schrodinger.ui.sequencealignment.dialogs
- 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.cmdline: Functions and classes to assist in standard processing of command line arguments.
- schrodinger.utils.config: A module for getting software configuration(web center urls for now)
- 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.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.openpdf: Display a PDF file.
- 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.subproc: A wrapper to the standard library subprocess module.
- schrodinger.utils.subprocess: A wrapper to the standard library subprocess module.
- schrodinger.utils.system: System-related utilities.
- schrodinger.utils.timers: Timer classes.
- schrodinger.utils.unicodesupport: Functions for encoding/decoding strings in files and paths
- schrodinger.utils.urllib: Functions that help access web URLs through proxy servers.

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

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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.