.. PyOR Documentation master file, created by
   sphinx-quickstart on Wed Apr 23 15:14:54 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to PyOR's Documentation!
=================================

**PyOR** (Python on Resonance)

*Motto:* **"Everybody can simulate Magnetic Resonance"**

**Author:** Vineeth Francis Thalakottoor Jose Chacko  

**Contact:** vineethfrancis.physics@gmail.com

**Github:** https://github.com/VThalakottoor/PyOR

About PyOR
----------

I developed **PyOR** during the early stages of my postdoc at École Normale Supérieure, Paris, purely for pleasure — to simulate NMR masers/rasers and assist individuals from physics, chemistry, and biology backgrounds in learning and simulating magnetic resonance experiments.  
PyOR is written entirely in Python because it is free, open-source, and widely accessible.

PyOR is particularly useful for:
- Beginners with a basic understanding of matrices, spin operators, and Python programming.
- Those interested in coding magnetic resonance pulse sequences and relaxation mechanisms.
- Educators using it as a tool to teach NMR principles to undergraduate and graduate students.

**Note:**  
While PyOR strives for accuracy, users should watch out for potential numerical inaccuracies and possible errors in theoretical equations.

Requirements
-------------

- Anaconda (Python Distribution, https://www.anaconda.com/download)
- Visual Studio Code (Editor, https://code.visualstudio.com/)
- Install `ipympl` to enable interactive matplotlib features:

  ```pip install ipympl```

Prerequisites
--------------

- Basic knowledge of Python programming (especially with **SciPy** and **NumPy**).
- Familiarity with object-oriented programming (OOP) concepts.
- Basic understanding of spin operators.

Recommended Reading
--------------------

- *Protein NMR Spectroscopy: Principles and Practice* — John Cavanagh et al.

Contents
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.. toctree::
   :maxdepth: 2
   :caption: Source Code

   modules

.. toctree::
   :maxdepth: 2
   :caption: Examples

   examples