Package schrodinger :: Package application

Package application


A package for application specific modules.

desmond:
    A package containing modules for the Desmond project

epik:
    A package exposing the Epik functionality.

glide:
    A package for creating Glide grid generation and docking jobs

inputconfig:
    Module for writing and reading simplified input files

jaguar:
    A package for creating Jaguar QM related tasks

ligprep:
    A package containing LigPrep-related modules.

macromodel:
    A package for creating and running MacroModel and Cluster jobs.

mcpro:
    A package containing modules for the MCPRO+ product

phase:
    A package containing Phase-related modules.

prepwizard:
    Module that is used by PrepWizard

report2d:
    Module that is used by 2D Viewer and generate_2d_report to produce
    PDF and HTML files with 2D structure images.

ska:
    Module for running SKA backend (protein structure alignment)

vsw:
    A package containing the VSW modules and stages

watermap:
    Module with WaterMap-related functions.

Submodules

[hide private]

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.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.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.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.msys: This is the high-level Python interface for msys, intended for use by chemists.
    - 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.inchi
    - 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.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.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.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: 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: 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.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 (.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
- 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.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
- 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.basiselements
- 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.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
- 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.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
- 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
- schrodinger.application.matsci.mecp_mod: Classes and functions for finding MECPs.
- schrodinger.application.matsci.montecarlo: Classes related to Monte Carlo simulations
- schrodinger.application.matsci.msicons
  - schrodinger.application.matsci.msicons.controlicons
- 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.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
- 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.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.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
  - 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.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.view_dialog
  - 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.jobs.clustal
  - schrodinger.application.msv.jobs.structure_alignment
- 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.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.phase_markers
- schrodinger.application.phase.phase_widgets
- schrodinger.application.phase.ui
  - schrodinger.application.phase.ui.feature_editor_ui
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

Variables

[hide private]

__package__ = None
hash(x)