- schrodinger.application.desmond.ana: Tools for various Desmond-related analyses.
- schrodinger.application.desmond.antlr3: @package antlr3
@brief ANTLR3 runtime package
- 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.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.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.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.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.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)
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