Welcome to rNets' Documentation!

rNets is an innovative python tool designed for visualization of reaction networks with a simple and robust command-line interface. rNets was conceptualized with the core principles of modularity, and easy integration with existing software packages by reducing dependencies to the minimum. This tool not only simplifies the visualization process but also opens new avenues for exploring complex reaction networks in diverse research contexts.

Quick Start

• Installation
  • Prerequisites
  • Installing the dependencies
  • Installing rNets
  • Uninstalling rNets
  • Developed with
• Basic Usage
• Command-line help
  • Named Arguments
  • Chemistry
  • Graph configuration
  • Edge configuration
  • Node configuration
• File Formats
  • Compounds File
    • Required columns
    • Optional columns
  • Reactions File
    • Required columns
    • Optional columns

Examples

• Command-line Examples
  • My first reaction graph
  • Drawing a thermodynamic graph
  • Drawing a kinetic graph
  • Using different energy units
  • Formatting our graph
• Python API Examples
  • My first Network
  • Drawing a thermodynamic graph
  • Drawing a kinetic graph
  • Using different energy units or temperature
  • Formatting our graph
  • Adding a colorbar legend
  • Integration with other software: Pykinetic (thermo)
  • Integration with other software: Pykinetic (kinetic)
• Published article
  • Imine condensation
    • Thermodynamic representations
    • Kinetic representations
    • An animation of the kinetic evolution
  • CO₂ hydrogenation on Pd(111)
    • Thermodynamic representations
    • Kinetic representations
  • Regiospecific CO₂ fixation
    • Preliminary steps
    • Quickstart
    • Generation of the network graph

Python API

• rnets
  • chemistry
  • colors
  • dot
  • parser
  • plotter
  • struct
  • addons

About

• Developers
• Citation
• Contribution

License

rNets is freely available under an MIT License

Indices and tables

• Index

• Module Index

• Search Page