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============
File Formats
============

The usage of pykinetic through the provided command line apps requires various 
text files following a specific formatting. The "Compounds" file and the 
"Reactions" file are always required. 

Compounds File
--------------

In this file the user specifies the compounds as well as their energies.

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   :start-after: compounds-start
   :end-before: compounds-end

Reactions File
--------------

In this file the user specifies the reactions and the Transition States (TS) or 
a manner of calculating the energy of the associated TS. 

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   :start-after: reactions-start
   :end-before: reactions-end

Simulation Parameters File
--------------------------

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