Package schrodinger :: Package application :: Package desmond

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Package desmond

Desmond-related modules.

The mdkey and mdc modules are just for the Desmond Panel.

Copyright Schrodinger, LLC. All rights reserved.

Submodules

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)

Variables

__package__ = None
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