.. ligand_param documentation master file, created by
   sphinx-quickstart on Thu Oct 10 16:49:20 2024.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to PharmaForge's documentation!
========================================

This is the documentation for the PharmaForge package, which is designed to store, process, and query molecular data in MongoDB. The 
dataset inclused hierarchical molecular information, making a NoSQL database like MongoDB the ideal choice for scalability and flexibility.

The workflow includes:

* Storing molecular data in MongoDB
* Processing the data using the PharmaForge package
* Labeling the data with the help of the PharmaForge package (e.g., adding SMILES notation)
* Querying the data using MongoDB's powerful query language
* Exporting the data to the DeepMD kit HDF5 format for MLP training.
* Relabeling data within the database using the PharmaForge package.


The design principles of the PharmaForge package are to make it easy to use, and flexible across a wide range of molecular systems, and easily queryable to find the data that you need. 

The package includes a robust interface to a wide-variety of electronic structure codes, including XTB, DFTB+, Gaussian, Psi4, and direct interfaces to the DeepMD-kit library as well. 

There is also a robust set of tools for querying the data within the database, through the querying api.

::

   >>> from pharmaforge.queries.Query import Query
   >>> query = "contains_elements only ['H', 'O']"
   >>> q = Query(query)
   >>> print(q.parsed_query)
   {'contains_elements': {'$not': {'$elemMatch': {'$nin': ['H', 'O']}}}}


Folder Structure
----------------
The folder structure of the documentation is as follows:


.. graphviz::
   :caption: Folder structure for the project.

   digraph G {
       rankdir=LR;
       node [shape=folder];

       "mldatabase" [label="mldatabase/"];
       "docs" [label="docs/"];
       "src" [label="src/"];
       "pharmaforge" [label="pharmaforge/"];
       "queries" [label="queries/"];
       "dbutils" [label="dbutils/"];
       "interfaces" [label="interfaces/"];
       "scripts" [label="scripts/"];
         "recipes" [label="recipes/"];
         "io" [label="io/"];
         "labeling" [label="labeling/"];
         "examples" [label="examples/"];

       "mldatabase" -> "docs";
       "mldatabase" -> "examples";
       "examples" -> "AddSmiles/"
       "examples" -> "DatabaseGeneration/"
       "examples" -> "QDPi1_Generation/";
       "examples" -> "QDPi2_Generation/";
       "examples" -> "DatabaseQuerying/";
       "examples" -> "CalculationInterfaces/";
       "examples" -> "Relabeling/";
       "examples" -> "CalculateMLP/";
       "examples" -> "Relabeling/";
       "mldatabase" -> "src";
       "src" -> "pharmaforge";
       "pharmaforge" -> "queries";
       "pharmaforge" -> "dbutils";
       "pharmaforge" -> "interfaces";
       "pharmaforge" -> "scripts";
       "pharmaforge" -> "recipes";
       "pharmaforge" -> "io";
       "pharmaforge" -> "labeling";
       "pharmaforge" -> "stats";


       node [shape=box];
       "pharmaforge" -> "DataBase.py";
       "dbutils" -> "create_mongodb_collections.py";
       "dbutils" -> "mongo_utils.py";
       "interfaces" -> "gaussianio.py";
       "interfaces" -> "xtbio.py";
       "interfaces" -> "psi4io.py";
       "interfaces" -> "deepmdio.py";
       "interfaces" -> "dftbio.py";
       "interfaces" -> "abstract.py";
       "interfaces" -> "deepio.py";
       "interfaces" -> "scanning.py";
       "scripts" -> "run_chunk_relabel.py";
       "recipes" -> "GeneralDatabase.py";
       "recipes" -> "QDPi1.py";
       "recipes" -> "QDPi2.py";
       "io" -> "hdf5_utils.py";
       "labeling" -> "get_smiles.py";
       "labeling" -> "relabeler.py";
       "labeling" -> "smiles.py";
       "queries" -> "Query.py";
       "stats" -> "comparator.py";
   }




Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

.. toctree::
   :maxdepth: 4
   :caption: User Documentation
   :numbered:

   ./documentation_pages/Installation.rst
   ./documentation_pages/QuerySyntax.rst
   ./documentation_pages/examples.rst



.. toctree::
   :maxdepth: 2
   :caption: Source Documentation
   :numbered:


   ./documentation_pages/DataBase.rst
   ./documentation_pages/Recipes.rst
   ./documentation_pages/io.rst
   ./documentation_pages/labeling.rst
   ./documentation_pages/dbutils.rst
   ./documentation_pages/interfaces.rst
   ./documentation_pages/queries.rst
   ./documentation_pages/stats.rst