.. _gettingstarted:

Getting started
===============

The functions that help analyzing data in the FAIRMD Lipids are described here. These
functions are located in the :mod:`fairmd.lipids` module. To get started using these
functions, first set up the package and initialize the databank:

.. code-block:: bash

   pip install nmrlipids_databank fmdl_initialize_data toy source databank_env.rc

"Toy" is a small test databank which is useful for testing and learning the package. You
can then start to work with the `template
<https://github.com/NMRLipids/databank-template/blob/main/scripts/template.ipynb>`_ or
write a code from the scratch. The minimum python code to intialize FAIRMD Lipids is

.. code-block:: python

   from fairmd.lipids.core import initialize_databank

   systems = initialize_databank()

After running this, ``systems`` is an instance of
:class:`fairmd.lipids.core.SystemsCollection` which works like a list but with added
functionality and contains dictionaries where each dictionary is a simulation in the
FAIRMD Lipids. A simulation dictionary contains the content of the README.yaml for that
simulation. The content of README.yaml files is described in :ref:`Simulation metadata
<readmesimu>`. ``systems`` can be then used to loop over all simulations:

.. code-block:: python

   for system in systems:
       print(system)

Examples on analyses over FAIRMD Lipids can be found from the `template
<https://github.com/NMRLipids/databank-template/blob/main/scripts/template.ipynb>`_ and
`codes used to analyze the results for the FAIRMD Lipids manuscript
<https://github.com/NMRLipids/DataBankManuscript/tree/main/scripts>`_.


The core functionality of the fairmd-lipids including initializing the database and the
definition of main data models is provided by :mod:`fairmd.lipids.core`. Some useful
functions for analysis of the simulations can be found in the
:mod:`fairmd.lipids.databankLibrary` module.


.. toctree::
   :maxdepth: 1

   api/exampleAndTutorials