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OpenFE Documentation

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  • Installation
  • Tutorials
  • User Guide
  • Cookbook
  • Reference
    • Changelog
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Site Navigation

  • Installation
  • Tutorials
  • User Guide
  • Cookbook
  • Reference
    • Changelog
  • GitHub

Section Navigation

  • Introduction
  • Simulation Setup
    • ChemicalSystems, Components and Thermodynamic Cycles
    • Creating Atom Mappings
    • Creating and using Protocols
    • Defining the Ligand Network
    • Alchemical Networks: Planning a Simulation Campaign
    • Alchemical Networks: Creation
  • Execution
    • Execution with Quickrun
    • Protocols and the Execution Model Theory
  • Working with Results
    • Working with individual results
    • Working with networks of results
  • CLI Interface
    • CLI basics
    • Customising CLI planning with YAML settings
  • Details of Specific Protocols
    • Relative Hybrid Topology Protocol
    • Absolute Solvation Protocol
    • Plain MD Protocol
  • Troubleshooting Simulations
  • User Guide
  • CLI Interface

CLI Interface#

In addition to the powerful Python API, OpenFE provides a simple command line interface to facilitate some more common (and less complicated) tasks. The Python API tries to be as easy to use as possible, but the CLI provides wrappers around some parts of the Python API to make it easier to integrate into non-Python workflows.

  • CLI basics
  • Customising CLI planning with YAML settings
    • Customising the atom mapper
    • Customising the network planner

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